Question: Approaches for DESeq2 analysis with one factor and many levels
0
gravatar for fl
6 months ago by
fl0
fl0 wrote:

Hello,

I am interested in using DESeq2 to analyze a bulk RNA-seq dataset with one factor and 12 levels (control and treatments), and 4 biological replicates per level. I was wondering how using one or multiple input sample tables would influence the genes that are found to be differentially expressed. For example, 1) I could provide a single table of sample information and then look at the possible pairwise contrasts between control and treatment levels. Alternatively, 2) I could provide multiple sample tables, one for each control-treatment pair. Will there be major differences in the genes found to be differentially expressed between either approach for the same control-treatment comparison?

I would be grateful for any insights/suggestions.

deseq2 • 110 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by fl0
Answer: Approaches for DESeq2 analysis with one factor and many levels
0
gravatar for Michael Love
6 months ago by
Michael Love23k
United States
Michael Love23k wrote:

This is a FAQ in the DESeq2 vignette. 

ADD COMMENTlink written 6 months ago by Michael Love23k
Answer: Approaches for DESeq2 analysis with one factor and many levels
0
gravatar for fl
6 months ago by
fl0
fl0 wrote:

Thank you, Michael.

ADD COMMENTlink written 6 months ago by fl0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour