Question: Remove batch effect for many RNA-seq
gravatar for Shaway
8 months ago by
Shaway0 wrote:

Hello every,

I a new comer for RNA-seq, here I have some questions for RNA-seq analysis.

I want to analyze about 10 type immune cells (more than 100 samples) and find the differential expressed genes. Now, I know that these data are from 12 different paper, I treat this as 12 batch then want to remove batch effect cause by different experiment.

Is it right for my understanding about batch effect?

Or I can do DE analysis just using TPM generated from raw counts.

Thank you, everyone!!

batch effect rna-seq combat sva • 357 views
ADD COMMENTlink written 8 months ago by Shaway0
gravatar for RamRS
8 months ago by
Houston, TX
RamRS26k wrote:

You should model the batch as a covariate in differential expression analysis. Avoid ComBat if you can, I don't think "removing" batch effect is all that effective. IMO.

You could also use ComBat on TPM, but be careful in interpreting the results.

ADD COMMENTlink written 8 months ago by RamRS26k

Thanks for your help!

ADD REPLYlink written 5 months ago by Shaway0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1491 users visited in the last hour