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2.8 years ago
lopes-santosg
•
0
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?
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.