Question: Deseq2 interaction results
0
gravatar for frimz.r
5 months ago by
frimz.r0
frimz.r0 wrote:

Dear Michael,

I have two Intereventions (HIgh protein and low protein diet) which i fed to individUals for 10 weeks, so i have 2 time points (PRE AND POST) . Simply i have 4 groups

Pre , Post Low diet, pre and post high diet.

i used deseq2  using this code 

ddsTC <- DESeqDataSetFromMatrix(countDatanew, colData=phenotype_data, ~ intervention + Time + intervention:Time)
ddsTC$intervention <- relevel(ddsTC$intervention, ref="control")
ddsTC$Time <- relevel(ddsTC$Time, ref="pre")
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ intervention + Time)

and i was wondering does my formula takes into account within subject comparison

ADD COMMENTlink modified 5 months ago by Michael Love22k • written 5 months ago by frimz.r0
Answer: Deseq2 interaction results
0
gravatar for Michael Love
5 months ago by
Michael Love22k
United States
Michael Love22k wrote:

If you don’t provide subject in the design then it doesn’t account for it. Can you paste your sample info table (colData) so we can see how the samples are distributed?

ADD COMMENTlink written 5 months ago by Michael Love22k
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