microarray data analysis a practical example using gepas
Post on 22-Dec-2015
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![Page 1: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/1.jpg)
Microarray data analysis
A practical example using GEPAS
![Page 2: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/2.jpg)
The GEPAS website
http://gepas.bioinfo.cipf.es/
![Page 3: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/3.jpg)
Tools roadmap
![Page 4: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/4.jpg)
Data exploration (input)
• Go to Tools Viewers Raw data viewer• Select the data from your computer• Check desired options, Name your job and Press “Run”. • The data will be first loaded and then processed. • Wait until you see a green label (with the job name) in the upper right corner of the window.
![Page 5: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/5.jpg)
Data exploration (output-I)
![Page 6: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/6.jpg)
Data exploration (output-II)
![Page 7: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/7.jpg)
• Go to Tools --> Normalization --> Affymetrix• Select your data (.CEL files compressed in a .zip or .gz
file) – If you have already uploaded your data press "select files from
the server" – If you haven't uploaded your data yet press "select files from
your computer"
• Leave default options – background correction-rma – normalization - quantiles– PMcorrection - pmonly– summarization -median polish
• Give the job a name, such as Kidney - Normalization and press "run"
Data Normalization (I)
![Page 8: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/8.jpg)
Data Normalization form (input)
![Page 9: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/9.jpg)
Data Normalization output (I)
![Page 10: Microarray data analysis A practical example using GEPAS](https://reader036.vdocuments.us/reader036/viewer/2022062314/56649d7e5503460f94a6065e/html5/thumbnails/10.jpg)
Data Normalization output (II)