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Batch effect

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.

rnaseq batch-effect

2 answers

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.

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

~ batch + condition

please read this paper:

ComBat-seq

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