I have some RNA-seq data I'm trying to do DESeq2 analysis on, and it's more complicated than what I've done before.
Patients came in two different times and had their blood drawn and sequenced. There is some missing data, so that some patients only have data for visit 1 or 2. In between visits patients were given either a placebo or one of two treatments.
The answer we're trying to answer is what expression levels changed in between visits in a different way between the treatment groups. Based on the vignettes and other answered questions it seems the design would be:
~ patient + visit + treatment + visit:treatment
the interaction visit:treatment would be the 'difference in differences' of each treatment over the time between visits. Is this correct?
Patients came in two different times and had their blood drawn and sequenced. There is some missing data, so that some patients only have data for visit 1 or 2. In between visits patients were given either a placebo or one of two treatments.
The answer we're trying to answer is what expression levels changed in between visits in a different way between the treatment groups. Based on the vignettes and other answered questions it seems the design would be:
~ patient + visit + treatment + visit:treatment
the interaction visit:treatment would be the 'difference in differences' of each treatment over the time between visits. Is this correct?
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