I have .gpr files from a 2-channel array (Phalanx Human OneArray) experiment in which only Cy5 was used. 6 arrays: n=3 each treatment and control. (Data was originally analyzed with Rosetta, but not going there.)
--This block of code runs fine, populating both the Red and Green columns with values (Red, Green, Red background, Green background, genes, etc).
RGuw <- read.maimages(targets, source="genepix")
RGw <- read.maimages(targets, source="genepix", wt.fun=wtflags(weight=0,cutoff = -50))
Control & empty probes are easily identifiable from gene IDs
Not sure how to proceed as far as
** Background subtraction
** Within +/- across array normalization
** As far as running limma, should I extract the Cy5 values and use a simple 1-column design matrix or submit the entire object and somehow code Cy3 & Cy5 columns so Cy3 is ignored or cancels out?
Thanks very much for any advice.