Question: Batch effects and MDSPlot in limma
gravatar for sonayuv
11 months ago by
sonayuv0 wrote:


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?

mds limma batcheffects galaxy • 451 views
ADD COMMENTlink written 11 months ago by sonayuv0

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

ADD REPLYlink written 11 months ago by Benn8.0k

Relevant post:

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

ADD REPLYlink written 11 months ago by h.mon30k
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