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.
