Question: DESeq2 pairwise comparison vs contrast function
0
gravatar for dequattro.concetta
4 months ago by
Italy
dequattro.concetta0 wrote:

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 • 202 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by dequattro.concetta0
Answer: DESeq2 pairwise comparison vs contrast function
0
gravatar for Michael Love
4 months ago by
Michael Love26k
United States
Michael Love26k wrote:

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

ADD COMMENTlink written 4 months ago by Michael Love26k
Answer: DESeq2 pairwise comparison vs contrast function
0
gravatar for dequattro.concetta
4 months ago by
Italy
dequattro.concetta0 wrote:

I found it. Thank you.

ADD COMMENTlink written 4 months ago by dequattro.concetta0
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