RNA-seq Differential expression using 3 groups

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BM • 0

@bm-8458

Last seen 8.8 years ago

United Kingdom

Hi,

I would like some advice on RNA-seq analysis. I have three groups (control, mutant 1 and mutant 2). we would like perform a one-way anova/GLM and to analyse all three groups pair wise. So analyse all three groups to test for significance, then esablish if any gene is changed bewteenany of the groups: control vs mutant 1; control vs mutant 2; mutant 1 vs mutant 2. However, we are running into problems.

Is it possible to do this in DESeq2 or EdgeR, or should iuse Genespring or Partek?

Thanks

rnaseq anova deseq2 edger genespring • 3.5k views

ADD COMMENT • link 8.8 years ago BM • 0

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Both DESeq2 and edgeR are quite capable of doing the analysis you describe. However 'we are running into problems' is completely non-specific, and is not near enough information for anybody to be able to help you.

Have you read the edgeR user's guide or the DESeq2 vignette? Both documents are quite comprehensive and in my opinion required reading for anybody who is planning to use either package.

ADD REPLY • link 8.8 years ago James W. MacDonald 65k

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