Question: Remove batch effect for many RNA-seq
gravatar for Shaway
19 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 • 741 views
ADD COMMENTlink written 19 months ago by Shaway0
gravatar for Ram
19 months ago by
Baylor College of Medicine, Houston, TX
Ram32k 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 19 months ago by Ram32k

Thanks for your help!

ADD REPLYlink written 16 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: 2070 users visited in the last hour