Question: Question about analysis design in DeSeq2
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gravatar for jillianrjaycox
2.2 years ago by
jillianrjaycox0 wrote:

I have cells from 5 healthy patients and 5 disease patients. Cells from each patient were treated with control and treatment conditions.

I would like to do differential expression analysis via DeSeq2 to understand how healthy vs. disease state affects the differential expression of genes between the control and treatment conditions. Within this, I need to control for the patient being the same between each control and treatment condition pair.

I have successfully figured out how to use Deseq2 for a simple analysis (eg just looking at how disease/healthy affect differential expression in the treatment group ONLY as ~Disease), but how would I specify the analysis described above?

Thanks!

rna-seq deseq2 • 683 views
ADD COMMENTlink modified 2.2 years ago by caggtaagtat1.1k • written 2.2 years ago by jillianrjaycox0

Section 4.1 of the EdgeR manual gives an example of disease with matched control samples. Yes, that's a different package, but DESeq2 will work exactly the same.

ADD REPLYlink written 2.2 years ago by Devon Ryan96k

Be aware that the section 4.1 example is for tumour vs normal comparisons nested within patients, not for the comparison of diseased and undiseased individuals where there is not an explicit matching between pairs of control individuals and diseased individuals

ADD REPLYlink written 2.2 years ago by russhh5.5k

It looks like OP has a nested design as well (treated and untreated cells in each patient), but yes the models won't be exactly the same.

ADD REPLYlink written 2.2 years ago by Devon Ryan96k
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