Question: Removing batch effects from RPKM data
gravatar for Apoorva
4.9 years ago by
United States
Apoorva260 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 4.9 years ago by andrew.j.skelton736.0k • written 4.9 years ago by Apoorva260
gravatar for andrew.j.skelton73
4.9 years ago by
andrew.j.skelton736.0k wrote:

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

ADD COMMENTlink modified 10 months ago by RamRS30k • written 4.9 years ago by andrew.j.skelton736.0k
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