Question: Batch effects and MDSPlot in limma
0
gravatar for sonayuv
5 weeks ago by
sonayuv0
sonayuv0 wrote:

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?

mds limma batcheffects galaxy • 137 views
ADD COMMENTlink written 5 weeks ago by sonayuv0
1

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

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1443 users visited in the last hour