Question: Batch effects and MDSPlot in limma
gravatar for sonayuv
5 weeks 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 • 137 views
ADD COMMENTlink written 5 weeks ago by sonayuv0

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

ADD REPLYlink written 5 weeks ago by Benn7.5k

Relevant post:

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

ADD REPLYlink written 5 weeks ago by h.mon27k
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