I am working with transcript counts produced by RSEM which gives me expected_count, TPM and FPKM values. I usually work with TPM values as the counts have been normalized for transcript length. I would like to use ComBat-seq for batch effect removal. The documentation https://github.com/zhangyuqing/ComBat-seq says ComBat-seq requires
untransformed, raw count matrix as input
It also says:
ComBat-seq provides adjusted data which preserves the integer nature of counts.
Since none of the counts produced by RSEM are integer, I'm not clear on what ComBat-seq is asking me to provide. It would seem that TPM would be appropriate as transcript length has been taken into account but the 'integer' part brings that into question.
Can anyone provide clarity on what I should pass into ComBat-Seq? thank you