How to select/exclude specific conditions or cell types for further analysis with Limma?

Question

[astromonocyte]

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)

[Kevin Blighe]

Evidently these are Illumina microarrays. I suspect that you can just leave them out of your targets file and not even process them. What are the contents of Einzelanalyse_nonorm_nobkgd.txt ?

[astromonocyte]

The "Einzelanalyse_nonorm_nobkgd.txt" are the results from the Illumina microarray, it contains 4 different columns for every probe.