Batch effect control in RNA-seq count data?

Hello DepMap,

I was wondering how the batch effect was controlled in the latest RNA-seq pipeline. Currently, you can download two different RNA-seq readouts; log-transformed TPM vs RSEM expected count. I was more interested in the RSEM count to use it as a count matrix input in DESeq2. But I just wanted to check if it makes sense to do that without knowing batch info, because the raw count might not have been controlled for batch effect. Thanks.


Apologies for the late reply! Currently DepMap doesn’t do any batch effect correction for the RNAseq data.