I am trying to visualise gene counts for a few interesting genes from an RNA-seq study. DESeq2's plotCounts gives me the counts against the conditions. For example,
I have 3 replicates, and there is a pronounced batch effect, as can be seen above. Firstly, is there a way to "cancel out" the batch effect in the plot. For the purpose of differential expression p-values, I have used a design matrix of ~ replicate + condition.
Secondly, should I instead plot the variance stabilized transformed counts? I don't think this has anything to do with batch effects, but if I am plotting a number of genes together, will it show them in the correct scale according to variance? Is there a way to plot the data from rlog(dds) for a gene?