gravatar for astromonocyte

2 hours ago by

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)



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