Validate TCGA DEGs with GEOdatabase
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7 days ago

Hey guys,

I need some help!

I'm working with TCGA-HNSC data using the TCGAbiolinks package which I already have previous experience. I downloaded and normalized the data. Later, I separated into low expression and high expression groups for DEG analysis. Now I would like to validate my DEGs using DEGs from other GEO banks - GSE65858, for example.

How should I proceed? Should I download raw data? Or download the standard available in GEO2R?

DEGs TCGA GEOdatabase • 100 views
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As long as you consider similar group of samples for comparison (similar design table) you should be fine to go. No matter using GEO2R or doing analysis by your own code.

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