Question: Correcting batch effects between RPKM datasets?
4
gravatar for JacobS
4.4 years ago by
JacobS900
Cleveland, Ohio
JacobS900 wrote:

I have two datasets, one with ~250 sample, and another with 7 samples. Both datasets are of RPKM values computed from human RNA-Seq. I don't have access to the primary reads files.

Is there a good way to batch-correct these datasets so that I can combine them and scan for expression signatures? I'm currently using an algorithm that creates a geometric average of the RPKM values for groups of genes that belong in a specific signature in order to compare samples, but the RPKM values of the ~250 sample dataset are on average much higher than the 7 sample dataset. 

I've used ComBat in the past for the same predicament but with microarray expression data, and it worked perfectly. I'm looking for something analogous for RPKM expression data.

dge rna-seq batch rpkm • 2.5k views
ADD COMMENTlink modified 4.3 years ago by Ying W3.9k • written 4.4 years ago by JacobS900

What are you going to do with the combined data?  If you are going to do differential expression analysis, what are the groups?

ADD REPLYlink written 4.3 years ago by Sean Davis25k
2
gravatar for Ying W
4.3 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

Have a look here What is the simple way to remove known batch effect from RNA-seq data ?

Combat should still work for RNA-seq, it can be found in the SVA package

You could also have a look at the following packages:

http://bioconductor.org/packages/release/bioc/html/sva.html

http://bioconductor.org/packages/release/bioc/html/RUVSeq.html

http://bioconductor.org/packages/release/bioc/html/EDASeq.html

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Ying W3.9k

Just note that batch effect correction is not always compatible with the experimental design and questions.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Sean Davis25k

Hi,

Thanks. That helps. But I was wondering if the input data in Combat would be just the RPKM data or log2 of the RPKM data

ADD REPLYlink modified 14 days ago by RamRS25k • written 4.1 years ago by ApoorvaB230
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