Question: Multiple factor design for differential expression with DESeq2
gravatar for galozs
29 days ago by
galozs0 wrote:


I am new to DESeq2 analysis and wondered if I could get a direction about the correct design for my experiment

I have counts tables (generated with FeatureCounts)

my samples where sorted for 2 markers and I have samples from 2 different tissues (with triplicates).


Tissue Marker1 Marker2
spleen pos pos
spleen pos neg
spleen neg pos
spleen neg neg
adipose pos pos
adipose pos neg
adipose neg pos
adipose neg neg


I would like to know:

1 - the effect of the markers and the interaction within each tissue

2- the difference between the effect between samples


How should I approach these questions? 

Should I split it into separate designs?

I am also concerned about if have enough power for multiple factor design (3 biological replicates)?



ADD COMMENTlink modified 28 days ago by Michael Love20k • written 29 days ago by galozs0
gravatar for Michael Love
28 days ago by
Michael Love20k
United States
Michael Love20k wrote:

Do you want to model the two markers also with an interaction? Or when you said interaction were you referring to each marker with tissue?

ADD COMMENTlink written 28 days ago by Michael Love20k
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