I'm new to R and Limma, and I tried to analyze a data set using the Limma guide. So far, so good, but now I want to include only 3 of the 6 cell types I have in my data set in "y" and any further analysis. How do I "select" or "exclude" conditions/cell types I defined in the targets file?
target file: column, 6 cell types, 4 donors
targets <- readTargets() x <- read.ilmn(files="Einzelanalyse_nonorm_nobkgd.txt",ctrlfiles="ControlProbeProfile_nonorm_nobkgd.txt") y <- neqc(x) expressed <- rowSums(y$other$Detection < 0.05) >= 3 y <- y[expressed,] plotMDS(y,labels=targets$condition)