Batch effects and MDSPlot in limma

Question

[sonayuv]

Hi,

I have 30 RNASeq samples from 2 different sets of experiments from different labs. It was suggested to do a check for batch effects in some threads. I used limma in galaxy to see the MDS plot of samples. Can somebody tell me how to identify if there is a batch effect from the MDS plot (preferably with a plot with and without batch effect) and how I should correct it in Galaxy?

[Benn]

There is an example in the user guide, page 137. Did you read that already?

https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

[h.mon]

Relevant post:

How to see if adjusting batch effect in RNA-seq is working or not