I am analyzing a RNA-seq data having some batch effect using DESeq2.
To account for the effect, I add it as a covariate to the regression model.
Next, to determine, how well the effect is corrected, I plot
two PCA plots
] - raw count
2. plotMDS(assays(dds)[["mu"]] - fitted values.
My question is: Is it the correct way to check how well the regression
model worked on accounting for the batch effect?