Question: Retrieving corrected matrix after linear model adjustment
0
gravatar for ahmed.asadik
19 months ago by
Germany, DKFZ
ahmed.asadik0 wrote:

Dear All,

I am using the limma package for differential expression analysis. In my datasets there are strong confounding effects due to both technical variation and biological contamination of the tumor cells with infiltrating cells and stroma.

I would like to cluster my patient samples after removing the confounders and for this I would need a matrix that has the new values after removing the confounding effects (similar to what ComBat is doing).

However, I have 10 covariate terms and 15 of their pairwise interactions and Combat doesn't allow for more than one Batch effect.

Could I use limma to fit a linear model including all covariates and then calculate a new matrix that would give the gene values after removing the confounders, Or is there some way to do this using sva?

I would really appreciate your reply, I have been scratching my head for a couple of days now.

Best,

Ahmed

 

limma sva • 295 views
ADD COMMENTlink modified 19 months ago by James W. MacDonald49k • written 19 months ago by ahmed.asadik0
Answer: Retrieving corrected matrix after linear model adjustment
0
gravatar for James W. MacDonald
19 months ago by
United States
James W. MacDonald49k wrote:

Yes. See ?removeBatchEffect

ADD COMMENTlink written 19 months ago by James W. MacDonald49k
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