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Microarray Data Analysis Using BASE
Danny Park
MGH Microarray Core
March 15, 2004
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You’ve got data!
What was I asking? – remember your experimental design
How do I analyze the data?– How do I find interesting stuff? – learn
some analysis tools– How do I trust the results? – statistics is
key
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What was I asking?
Typically: “which genes changed expression levels when I did ____”
Common ____:– Binary conditions: knock out, treatment, etc– Continuous scales: time courses, levels of
treatment, etc– Unordered discrete scales: multiple types of
treatment or mutations
This tutorial’s focus: binary experiments
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How do I analyze the data?
BASE – BioArray Software Environment– Data storage and distribution– Simple filtering, normalization, averaging,
and statistics– Export/Download results to other tools
MS Excel TIGR Multi Experiment Viewer (TMEV) This tutorial’s focus: using BASE
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Today’s Presentation
Demonstrate the most basic analysis techniques
Using our most frequently used software (BASE)
For the most common kind of experiments
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Work Flow
Images & data files
scan, segment
uploadBASE
Labeled cDNA
Slides
QC & label
hybridize
RNA
analysis
Researcher
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The Most Common experiment
Two-sample comparison w/N replicates– KO vs. WT– Treated vs. untreated– Diseased vs. normal– Etc
Question of interest: which genes are (most) differentially expressed?
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Experimental Design – naïve
A
B
From Gary Churchill, Jackson Labs
From Gary Churchill, Jackson Labs
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Experimental Design – tech repl
A
B
From Gary Churchill, Jackson Labs
From Gary Churchill, Jackson Labs
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Experimental Design – bio repl
Treatment
Biological Replicate
Technical Replicate
Dye
Array
A BA B
From Gary Churchill, Jackson Labs
From Gary Churchill, Jackson Labs
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The Most Common Analysis
Filter out bad spots Adjust low intensities Normalize – correct for non-linearities
and dye inconsistencies Filter out dim spots Calculate average fold ratios and p-
values per gene Rank, sort, filter, squint, sift data Export to other software
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BASE @ MGH
BASE is a microarray data storage and analysis package
BASE resides on our web server– Data is stored at our facility– Computation is performed on our machines
All you need is a web browser– https://base.mgh.harvard.edu/– A Microarray Core technician will provide you with
a username, password, and experiment name
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BASE – Login page
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BASE – Login page
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BASE – Login page
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BASE – Login page
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BASE – Logged in
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BASE – Logged in
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BASE – Sidebar
Reporters
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BASE – Sidebar
Reporters
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BASE – Sidebar
Array LIMS
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BASE – Sidebar
Array LIMS
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BASE – Sidebar
Biomaterials
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BASE – Sidebar
Biomaterials
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BASE – Sidebar
Hybridizations
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BASE – Sidebar
Hybridizations
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BASE – Sidebar
Analyze Data
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BASE – Sidebar
Analyze Data
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BASE – Sidebar
Users
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BASE – Sidebar
Users
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BASE – My Account
Change your password and access defaults
Change your password and access defaults
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BASE – My Account
Change your password and access defaults
Change your password and access defaults
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BASE – My Account
Change your password and access defaults
Change your password and access defaults
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BASE – My Account
Change your password and access defaults
Change your password and access defaults
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Find your experiment
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Find your experiment
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Find your experiment
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Find your experiment
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Experiment view: Four Tabs
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Group slide data together
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Group slide data together
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
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Group slide data together
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
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Group slide data together
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
Select the slides that measure the same thing. Later in analysis, they will be averaged together. In this experiment, all ten slides are replicates, so there is only one grouping.
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Group slide data together
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Group slide data together
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
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Group slide data together
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
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Group slide data together
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
Give your data set a descriptive name to distinguish it from other slide groupings. In this Myd88 knockout experiment, there is only one grouping, so a generic name is fine.
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Analysis: Begin
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Analysis: Begin
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Analysis: Begin
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Analysis: Begin
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Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
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Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 61: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/61.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 62: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/62.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 63: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/63.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 64: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/64.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 65: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/65.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 66: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/66.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
![Page 67: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/67.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
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Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
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Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 70: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/70.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 71: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/71.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 72: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/72.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 73: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/73.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 74: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/74.jpg)
Analysis: Filter Setup
“Bad” spots are marked with a negative Flag value.
“Bad” spots are marked with a negative Flag value.
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
Oligos are annotated with species codes, but control spots are not. Set species to your two-letter code of choice (Mm, Hs, Dr, Pa, etc)
![Page 75: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/75.jpg)
Analysis: Filter Setup
Naming the filter and the child data set are essential to reducing confusion later.
Naming the filter and the child data set are essential to reducing confusion later.
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Analysis: Filter Setup
Naming the filter and the child data set are essential to reducing confusion later.
Naming the filter and the child data set are essential to reducing confusion later.
![Page 77: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/77.jpg)
Analysis: Filter Setup
Naming the filter and the child data set are essential to reducing confusion later.
Naming the filter and the child data set are essential to reducing confusion later.
![Page 78: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/78.jpg)
Analysis: Filter Run
![Page 79: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/79.jpg)
Analysis: Quality Data
![Page 80: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/80.jpg)
Analysis: Quality Data
![Page 81: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/81.jpg)
Analysis: Unfiltered Data
![Page 82: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/82.jpg)
Analysis: Filter Parameters
![Page 83: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/83.jpg)
Analysis: Limit-Int Setup
![Page 84: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/84.jpg)
Analysis: Limit-Int Setup
![Page 85: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/85.jpg)
Analysis: Limit-Int Setup
![Page 86: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/86.jpg)
Analysis: Limit-Int Setup
![Page 87: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/87.jpg)
Analysis: Limit-Int Setup
![Page 88: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/88.jpg)
Analysis: Limit-Int Setup
![Page 89: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/89.jpg)
Analysis: Check job status
![Page 90: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/90.jpg)
Analysis: Check job status
![Page 91: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/91.jpg)
Analysis: Check job status
![Page 92: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/92.jpg)
Analysis: Check job status
![Page 93: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/93.jpg)
Analysis: Check job status
“All done” indicates the job is complete.
“All done” indicates the job is complete.
![Page 94: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/94.jpg)
Analysis: Check job status
“All done” indicates the job is complete.
“All done” indicates the job is complete.
![Page 95: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/95.jpg)
Analysis: Limit-Int Output
![Page 96: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/96.jpg)
Analysis: Limit-Int Output
![Page 97: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/97.jpg)
Analysis: Limit-Int Output
![Page 98: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/98.jpg)
Analysis: Limit-Int Output
![Page 99: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/99.jpg)
Analysis: Limit-Int Output
![Page 100: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/100.jpg)
Analysis: Limit-Int Output
![Page 101: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/101.jpg)
Analysis: Change data set name
![Page 102: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/102.jpg)
Analysis: Change data set name
![Page 103: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/103.jpg)
Analysis: Change data set name
Change the name of this set to “Intensity limited Data”
Change the name of this set to “Intensity limited Data”
![Page 104: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/104.jpg)
Analysis: Change data set name
![Page 105: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/105.jpg)
Analysis: Change data set name
![Page 106: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/106.jpg)
Analysis: Change data set name
![Page 107: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/107.jpg)
Analysis: Change data set name
![Page 108: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/108.jpg)
Analysis: LOWESS Setup
![Page 109: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/109.jpg)
Analysis: LOWESS Setup
![Page 110: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/110.jpg)
Analysis: LOWESS Setup
![Page 111: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/111.jpg)
Analysis: LOWESS Setup
![Page 112: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/112.jpg)
Analysis: LOWESS Setup
![Page 113: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/113.jpg)
Analysis: LOWESS Setup
![Page 114: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/114.jpg)
Analysis: Check job status
![Page 115: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/115.jpg)
Analysis: Check job status
![Page 116: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/116.jpg)
Analysis: LOWESS Output
![Page 117: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/117.jpg)
Analysis: LOWESS Output
![Page 118: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/118.jpg)
Analysis: LOWESS Output
Change the name of this set to “Normalized Data” using the same steps as before.
Change the name of this set to “Normalized Data” using the same steps as before.
![Page 119: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/119.jpg)
Analysis: Change data set name
Change the name of this set to “Normalized Data” using the same steps as before.
Change the name of this set to “Normalized Data” using the same steps as before.
![Page 120: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/120.jpg)
Analysis: Change data set name
Change the name of this set to “Normalized Data” using the same steps as before.
Change the name of this set to “Normalized Data” using the same steps as before.
![Page 121: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/121.jpg)
Analysis: Filter Setup
Set up the filter as indicated, hit Add/Update on the Gene filter, then hit Accept and select the resulting data set.
Set up the filter as indicated, hit Add/Update on the Gene filter, then hit Accept and select the resulting data set.
![Page 122: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/122.jpg)
Analysis: Useful Data
![Page 123: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/123.jpg)
Analysis: Useful Data
![Page 124: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/124.jpg)
MA Plots: Raw Myd88 Data
![Page 125: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/125.jpg)
MA Plots: Raw Myd88 Data
![Page 126: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/126.jpg)
MA Plots: Raw Myd88 Data
![Page 127: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/127.jpg)
MA Plots: Raw Myd88 Data
![Page 128: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/128.jpg)
MA Plots: Quality Data
![Page 129: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/129.jpg)
MA Plots: Quality Data
![Page 130: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/130.jpg)
MA Plots: Quality Data
![Page 131: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/131.jpg)
MA Plots: Quality Data
![Page 132: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/132.jpg)
MA Plots: Quality Data
![Page 133: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/133.jpg)
MA Plots: Quality Data
![Page 134: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/134.jpg)
MA Plots: Int-limited Data
![Page 135: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/135.jpg)
MA Plots: Int-limited Data
![Page 136: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/136.jpg)
MA Plots: Int-limited Data
![Page 137: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/137.jpg)
MA Plots: Int-limited Data
![Page 138: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/138.jpg)
MA Plots: Int-limited Data
![Page 139: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/139.jpg)
MA Plots: Int-limited Data
![Page 140: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/140.jpg)
MA Plots: Normalized Data
![Page 141: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/141.jpg)
MA Plots: Normalized Data
![Page 142: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/142.jpg)
MA Plots: Normalized Data
![Page 143: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/143.jpg)
MA Plots: Normalized Data
![Page 144: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/144.jpg)
MA Plots: Normalized Data
![Page 145: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/145.jpg)
MA Plots: Normalized Data
![Page 146: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/146.jpg)
MA Plots: Norm. Corr. Factor
![Page 147: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/147.jpg)
MA Plots: Norm. Corr. Factor
![Page 148: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/148.jpg)
MA Plots: Useful Data
![Page 149: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/149.jpg)
MA Plots: Useful Data
![Page 150: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/150.jpg)
MA Plots: Useful Data
![Page 151: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/151.jpg)
MA Plots: Useful Data
![Page 152: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/152.jpg)
MA Plots: Useful Data
![Page 153: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/153.jpg)
MA Plots: Useful Data
![Page 154: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/154.jpg)
Analysis: Useful Data
![Page 155: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/155.jpg)
Analysis: Useful Data
![Page 156: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/156.jpg)
Analysis: Fold Ratio Setup
![Page 157: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/157.jpg)
Analysis: Fold Ratio Setup
![Page 158: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/158.jpg)
Analysis: Fold Ratio Setup
![Page 159: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/159.jpg)
Analysis: Fold Ratio Setup
![Page 160: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/160.jpg)
Analysis: Fold Ratio Output
![Page 161: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/161.jpg)
Analysis: Fold Ratio Output
![Page 162: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/162.jpg)
Analysis: Fold Ratio Output
![Page 163: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/163.jpg)
Analysis: Fold Ratio Output
![Page 164: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/164.jpg)
Analysis: Fold Ratio Output
![Page 165: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/165.jpg)
Analysis: Fold Ratio Output
![Page 166: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/166.jpg)
Analysis: Fold Ratio Output
![Page 167: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/167.jpg)
Analysis: Fold Ratio Output
![Page 168: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/168.jpg)
Analysis: Change list name
![Page 169: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/169.jpg)
Analysis: Change list name
![Page 170: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/170.jpg)
Analysis: Change list name
Change the name of this list as indicated here.
Change the name of this list as indicated here.
![Page 171: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/171.jpg)
Analysis: Change list name
Change the name of this list as indicated here.
Change the name of this list as indicated here.
![Page 172: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/172.jpg)
Analysis: Change list name
![Page 173: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/173.jpg)
Analysis: Change list name
![Page 174: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/174.jpg)
Analysis: Fold Ratio Graphs
![Page 175: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/175.jpg)
Analysis: Fold Ratio Graphs
![Page 176: Microarray Data Analysis Using BASE Danny Park MGH Microarray Core March 15, 2004](https://reader030.vdocuments.us/reader030/viewer/2022013012/56649d245503460f949fb18e/html5/thumbnails/176.jpg)
Analysis: Fold Ratio Graphs
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Analysis: Fold Ratio Graphs
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Analysis: Fold Ratio Graphs
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Analysis: Fold Ratio Graphs
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Analysis: t-test Setup
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Analysis: t-test Setup
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Analysis: t-test Setup
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Analysis: t-test Setup
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Analysis: t-test Output
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Analysis: t-test Output
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Analysis: t-test Output
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Analysis: t-test Output
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Analysis: t-test Output
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Analysis: t-test Output
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Analysis: Change list name
Change the name of this set to “myd88 p-value” using the same steps as before.
Change the name of this set to “myd88 p-value” using the same steps as before.
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Analysis: Change list name
Change the name of this set to “myd88 p-value” using the same steps as before.
Change the name of this set to “myd88 p-value” using the same steps as before.
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Analysis: Change list name
Change the name of this set to “myd88 p-value” using the same steps as before.
Change the name of this set to “myd88 p-value” using the same steps as before.
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Analysis: t-test Graphs
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Analysis: t-test Graphs
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Analysis: t-test Graphs
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Analysis: t-test Graphs
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Analysis: t-test Graphs
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Analysis: t-test Graphs
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Analysis: Experiment Explorer
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Analysis: Experiment Explorer
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
Fill out the table as indicated, then hit Add/Update.
Fill out the table as indicated, then hit Add/Update.
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: Gene List View
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EExplore: NCBI Links
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EExplore: Gene List ViewThis additional row will restrict hits to P values of 5% or less.
This additional row will restrict hits to P values of 5% or less.
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EExplore: Gene List ViewThis additional row will restrict hits to P values of 5% or less.
This additional row will restrict hits to P values of 5% or less.
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Single Gene View
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EExplore: Gene List View
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EExplore: Gene List View
Open MS Excel and tell it to open the file you downloaded (typically called base.tsv).
Open MS Excel and tell it to open the file you downloaded (typically called base.tsv).
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EExplore: Gene List View
Open MS Excel and tell it to open the file you downloaded (typically called base.tsv).
Open MS Excel and tell it to open the file you downloaded (typically called base.tsv).
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Have Fun!
The rest of the analysis is largely driven by your biological understanding of the genes indicated in these lists. We cannot help much in the interpretation of this data.
Don’t forget to go back to the raw data sets and repeat this entire analysis for any other slide groupings.
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Acknowledgements
MGH Lipid Metabolism UnitMason FreemanHarry Bjorkbacka
MGH Lipid Metabolism UnitMason FreemanHarry Bjorkbacka
LUND (Sweden) Dept. Theoretical Physics & Dept. OncologyCarl TroeinLao H. SaalJohan Vallon-ChristerssonSofia GruvbergerÅke BorgCarsten Peterson
LUND (Sweden) Dept. Theoretical Physics & Dept. OncologyCarl TroeinLao H. SaalJohan Vallon-ChristerssonSofia GruvbergerÅke BorgCarsten Peterson
MGH Microarray CoreGlenn ShortJocelyn BurkeNajib El MessadiJason FrietasZhiyong Ren
MGH Microarray CoreGlenn ShortJocelyn BurkeNajib El MessadiJason FrietasZhiyong Ren
MGH Molecular Biology Bioinformatics GroupChuck CooperXiaowei Wang
Harvard School of Public Health BiostatisticsXiaoman Li
MGH Molecular Biology Bioinformatics GroupChuck CooperXiaowei Wang
Harvard School of Public Health BiostatisticsXiaoman Li