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Question: Remove batch effect for differential expression
1
gravatar for Ron
3.5 years ago by
Ron • 990
United States
Ron • 990 wrote:

Hi,

I want to do differential expression between two groups(two batches).For clustering analysis of these samples from two groups,I did batch normalization using COMBAT (sva package)on expression values so as to remove batch effects.

But for differential expression,should I do batch normalization as well before proceeding, as DEseq expects raw counts ? Or is there any way DEseq bioconductor takes into account for different batches and does normalization,before doing differential expression?

Any suggestions,please?

Thanks,

Ron
rna-seq deseq next-gen R • 4.4k views
ADD COMMENT • link •
modified 3.5 years ago by WouterDeCoster ♦ 43k • written 3.5 years ago by Ron • 990
2
gravatar for WouterDeCoster
3.5 years ago by
WouterDeCoster ♦ 43k
Belgium
WouterDeCoster ♦ 43k wrote:

Assuming you did a proper design and treatments are distributed over batches (not all treatment A in batch 1 and treatment B in batch 2 but mixed) you can specify the batch in the design formula and this will be taken into account by DESeq2 and similar tools.

An example of a discussion about a design like that can be found at correcting for a batch in DESeq2 and https://support.bioconductor.org/p/76099/ (among many more)
ADD COMMENT • link written 3.5 years ago by WouterDeCoster ♦ 43k

Hi WouterDeCoster,

I read this post,that I can use Combat batch normalization on Counts and then used the normalized values for differential expression with limma (not EdgeR and DESeq). What do you think on this?

ADD REPLY • link written 3.4 years ago by Ron • 990

Don't use Combat. Go by Wouter's advice, i.e., to include batch in the design model / formula.

If you need even more advice, then take that of one of the core developers of Limma himself:

ADD REPLY • link modified 2.1 years ago • written 2.1 years ago by Kevin Blighe ♦ 59k

Hi WouterDeCoster,

How to deal with batch effects in this situation (all treatment A in batch 1 and treatment B in batch 2)? Specifying batch in the design formula gives error. Is it even possible to remove in that case?

ADD REPLY • link written 11 months ago by kunal368 • 0
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