Hi everybody,
I have question on repeated measure analysis using edegR or DESeq.
The experiment contains two groups (low and good) and three time point(0 day, 14 day, and 28 day) from 6 individuals in each group (i.e. repeated in each time; in total 36 samples). I want to check which gene is differentially expressed within the group between time points and between groups at different time point.
I am think to analyse using a mixed-model nested repeated measures.
where;
quality = main effect (i.e. good or low - fixed)
individuals(quality) = individual nested within quality (random factor)
time = fixed factor and repeated factor
time x quality = fixed factor
time x individual(quality) = random factor
Is this sound ok? If so, can I model it in edgeR as it is mentioned in section 3 of user guide, like this:
quality <- factor(DATA$quality, levels=c("good", "low"))
time <- factor(DATA$time, levels=c("0day","14day","28day"))
design <- model.matrix(~quality+quality:individual+quality:time)
How the contrast argument works for example to compare good:0day vs low:0day? Should I relevel the base to 14 day or 28 day to get the contrast among time points?
Thanks
I have question on repeated measure analysis using edegR or DESeq.
The experiment contains two groups (low and good) and three time point(0 day, 14 day, and 28 day) from 6 individuals in each group (i.e. repeated in each time; in total 36 samples). I want to check which gene is differentially expressed within the group between time points and between groups at different time point.
I am think to analyse using a mixed-model nested repeated measures.
where;
quality = main effect (i.e. good or low - fixed)
individuals(quality) = individual nested within quality (random factor)
time = fixed factor and repeated factor
time x quality = fixed factor
time x individual(quality) = random factor
Is this sound ok? If so, can I model it in edgeR as it is mentioned in section 3 of user guide, like this:
quality <- factor(DATA$quality, levels=c("good", "low"))
time <- factor(DATA$time, levels=c("0day","14day","28day"))
design <- model.matrix(~quality+quality:individual+quality:time)
How the contrast argument works for example to compare good:0day vs low:0day? Should I relevel the base to 14 day or 28 day to get the contrast among time points?
Thanks
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