Question: Deseq2 interaction results
gravatar for frimz.r
22 days ago by
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 22 days ago by Michael Love19k • written 22 days ago by frimz.r0
gravatar for Michael Love
22 days ago by
Michael Love19k
United States
Michael Love19k 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 22 days ago by Michael Love19k
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