For RNA-seq data analysis using DESeq2, a recommended method for batch effect removal is to introduce the batch in the design of the experiment as
design = ~ batch + condition.
The presence of batch was already known from experiment design and also detected by PCA biplot on the log transformed raw counts. Post DESeq2 how can we assure that the batches have been correctly taken care of? PCA plot on
counts(dds, normalized=TRUE) did not how any changes.
Correcting the batch using ComBat brings out the desired grouping, however, I understand the output from Combat should not be used with DESeq2. Is there any other suggested tool for differential gene expression analysis post batch correction using ComBat?