Hi, there

I downloaded RSEM expected_count data of TCGA TARGET GTEX from UCSC Xena to perform differential expressed analysis. I noticed the unit is log2(x+1), but I failed to turn the data into integers. The input of DESeq2 should be a matrix with integers. Any suggestions? Thanks in advance!

Best,

Issac
log2(x+1) data is not suitable for analysis with DESeq2 (nor edgeR/voom). So you would at least have to convert it back to counts by doing (2^x) -1. You could then simply round to the nearest integer. Alternatively you can download un-tarnsformed RSEM output from Firehose at https://gdac.broadinstitute.org/