**0**wrote:

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

1. plotMDS(assays(dds)[["counts"]

] - 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?

**17k**• written 3.6 years ago by Sachin Pundhir •

**0**