Question: Removing batch effects from RPKM data
gravatar for ApoorvaB
4.4 years ago by
United States
ApoorvaB240 wrote:

Hi everyone,

I am doing RNA-Seq data analysis on 22 samples from 3 batches. I have the RPKM values of all the samples. I performed PCA and I found some batch effect. I would like to remove the batch effect so that I can go ahead with differential expression analysis.

I was reading some posts and I saw that the removeBatchEffect() function in the limma package of bioconductor has been used a lot with count matrix. Can i use this function with a matrix containing RPKM values? In that case, will the result also be a matrix containing RPKM values with just the batch effects removed ? Also, should I take log2 values of the RPKM ?


ADD COMMENTlink modified 4.4 years ago by andrew.j.skelton735.9k • written 4.4 years ago by ApoorvaB240
gravatar for andrew.j.skelton73
4.4 years ago by
andrew.j.skelton735.9k wrote:

The short answer is no. I suggest you look at the discussions in your own post on Bioconductor Support:

ADD COMMENTlink modified 4 months ago by RamRS26k • written 4.4 years ago by andrew.j.skelton735.9k
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