Hi,
I am trying to follow the TCGAbiolinks Vignette in the "Analyze the data" section about differential expression and enrichment analysis, but I am running into a problem. When I load the dataset dataBRCA which is included in the TCGAbiolinks library, the enrichment analysis from the vignette works; When I download and use my own data using the functionality provided by TCGAbiolinks, it does not work (it says ResBP=NA, ResMF=NA, ResCC=NA, ResPat=NA). In the vignette, I noticed that the dataBRCA is normalized using the TCGAanalyze_Normalization function with the geneInfo = geneInfo option, while my data is HTSeq - counts, and must be normalized with the geneInfo = geneInfoHT option. What is the difference between the two options, and could this be the problem?
Thanks David
