Batch effect

Question

[Fatemeh]

Dear all,

I am going to use RNA seq data from other groups that their count read tables are available.

However, I have no idea how to do batch effect. I am not a bioinformatician but I can use R for DESeq analysis and enrichment analysis. I would appreciate if you explain it simple that I can follow.

Thanks very much for your help.

Answer 1

[swbarnes2]

Just add batch to the design in DESeq.

But if your batch is confounded with an experimental condition, there is no magic trick to fix that.

[Fatemeh]

I did not understand what do you mean by adding the batch in DESeq. Could you please explain more? Thanks very much.

[Picasa]

~ batch + condition

Answer 2

[pinheirofabiano]

please read this paper:

ComBat-seq

[Fatemeh]

Thanks very much.