I intend to analyze differential gene expression using a GEO dataset. The value is log2 normalized signal intensity.
I know edgeR's workflow involves log normalization. However, can I skip the normalization steps and continue the rest of the analysis (estimate the BCV(s) and make pairwise comparisons)? Or do I need to analyze from scratch (raw data)?
I have read the user's guide and searched online, but I did not find an answer to my question.
Thank you very much for any help you can provide. Have a nice day!
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, you can't use edgeR. If the data set is derived from sequencing and involves read counts, edgeR might be appropriate if you can get read counts on features. (all the stuff that LChart said).
That explains a lot to me. Thank you, seidel! They used Affymetrix Human Gene 1.0 ST Array chips.
Hope you have a wonderful day.