I was wondering how to run the
lfcShrink() when my
resultsNames() doesn't list the comparisons I would like to do.
I have a data set with four different conditions within each of my two time-points. For my comparisons I would like to compare the four conditions within each of the timepoints against each other. As for a control condition, i have one for each of the two timepoints.
resultsNames() function doesn't list all of the wanted comparisons.
my conditions are listed below
condition <- factor(rep(c("GFPMinus24","GFPPlus24","ArtMinus24", "ArtPlus24","Q97Plus24","Q97Minus24","GFPMinus40","GFPPlus40","ArtMinus40", "ArtPlus40","Q97Plus40","Q97Minus40"),each=3)) ## or creating the three different vectors separately Agg <- factor(rep(rep(c("Minus", "Plus"), each = 6), each = 3) ) group <- factor(rep(c("GFP", "Art", "Q97"), each = 12) ) TP <- factor(rep(rep(c(24, 40), each = 3), each = 6))
GFP samples are my (sort of) control I'm also comparing Art vs. Q97 samples.
Plus state whether or not an additional compound was added, while the
Q97 stands for another additional aggregate.
So I'm not sure how to build my model.matrix here to include all the coefficients in
Would it make more sense (and easier to handle ) to analyze the different situations on a pair-wise basis? If not, can someone please help me to create a model.matrix for the various comparisons?