Validate TCGA DEGs with GEOdatabase
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?
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Hamid Ghaedi
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lopes-santosg •
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lopes-santosg •
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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.