DESeq2 pairwise comparison vs contrast function
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@dequattroconcetta-21510
Last seen 2.1 years ago
Italy

Hi,

Briefly, I want to identify differentially expressed genes from RNA-seq data using DESeq2.

I have three conditions and I want to compare the three conditions to each other.

Usually, I perform pairwise comparison building the dds file with the two conditions that I want to compare and subsequently I run DESeq2 on the dds object. I would like to ask if there are any differences between two approaches:

  1. Approach 1: perform separately each pairwise comparison as I described above
  2. Approach 2: perform the analysis including the three conditions in the dds object and then run the contrast function to extract the comparison that I want to analyse.

In particular, are there any differences between the two approaches in the normalization of count data and in the differential expression analysis? For example, if I have a condition with more variability than the other two conditions, this can affect the identification of differentially expressed genes in Approach 2? In addition, I was wondering if the Approach 1 is able to highlight more differences, even the smallest one between the conditions, in comparison with the results obtained from the Approach 2.

Thank you!

Concetta

deseq2 • 2.1k views
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@mikelove
Last seen 2 hours ago
United States

This was just asked in a very recent thread on the support forum. See 'Latest' above.

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Hi, I'm also having this question because I get two very different adjusted p-value with pairwise comparison and contrast function (for the same dataset). Could you help me understand what's the better approach?

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See the FAQ in the vignette.

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@dequattroconcetta-21510
Last seen 2.1 years ago
Italy

I found it. Thank you.

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