Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integers?

Question

[dz2353]

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

Answer 1

[i.sudbery]

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/

[dz2353]

Yep, I did (2^x)-1 but the result is not an integer format cause the scale. I will round them. Thanks a lot!