Question: DESeQ2 design multiple conditions
0
gravatar for domenicoalessandrosilvestris
5 weeks ago by

Hi,

I'm using DESeq2 with 4 multiple conditions ("A", "B", "C" and "D"), but I'm only interested in the comparisons A vs C; A vs D; B vs C and B vs D. Since the higher the number of tests performed and the lower the significant results (and the "contrast" argument of the result function performs only a filtering I think) I wondered if there was a way to set the "desing" avoiding that are all possible comparisons in pairs between conditions performed? Thank you very much in advance to anyone who wants to help me !!

Alessandro

deseq2 • 109 views
ADD COMMENTlink modified 5 weeks ago by swbarnes2200 • written 5 weeks ago by domenicoalessandrosilvestris0
Answer: DESeQ2 design multiple conditions
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gravatar for swbarnes2
5 weeks ago by
swbarnes2200
swbarnes2200 wrote:

Have you read any vignettes or tutorials? If you are thinking that the default setting is to do all 6 comparisons and mash the results together, it's not. The simplest way to run the software is to specify which two groups you want to compare to each other, and do that 4 times to get 4 sets of results.

ADD COMMENTlink written 5 weeks ago by swbarnes2200

Thanks for the reply! I know that your solution is obviously the simplest but in that way when you extract the normalized counts you get slightly different values ​​for the same gene in the same sample depending on the comparison you are considering and if you have to use these values ​​for example then in a correlation you will have a little problem..

Alessandro

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by domenicoalessandrosilvestris0

No, you don't. You don't have to subset the data to compare one sub group to another. Run DESeq on the whole dds object, then do the comparison you want with contrasts.

ADD REPLYlink written 5 weeks ago by swbarnes2200

From what I understand "contrast" extracts only the results related to the comparison you are requesting, but the actual statistical test is performed by the "DESeq" function in fact when I go to open the dds it tells me "assays (6)". Actually the problems are two: to avoid making thousands of useless statistical tests (if not harmful) and to have a unique expression value for each gene in each sample. Thanks again!

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by domenicoalessandrosilvestris0
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