Nowadays, I want to utilize the pan-cancer dataset "EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2" for DEGs analysis. Because of the normalized and batch corrected transformation, I would perfer to use limma::voom. However, the dataset contains negative value, which isn't accepted by limma::voom. Any advices for dealing with those negative values before DEGs analysis? Thanks in advance!
It isn't clear what data you are trying to analyse. Please give a link to the data that you downloaded and explain what sort of data it is (counts, rpkm, tpm etc).
Thanks for your reply sir! Here is the data (EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv). And there is the data procession of this data. Thanks a lot sir!