Hi,

SORRY, but I have a very basic question on dye swap.

A set of cDNA microarray samples contains a few dye-swaps. For
retrieving normalized, log2 transformed expression values (against a common
reference for all samples), I wonder how I can make sure that the
“dye-swap”-nature of the files is taken into account as I get the final
spreadsheet of the expression values for all the Genepix files !

I have gone through limma which talks about fitting a linear model for each
gene using design matrix. But, I wish to know just the  expression values of
the files (with dye-swaps taken care of in the final output).

Please provide some suggestion(s)/pointer(s).

Thanks a lot !

Cheers,
Christina


*The codes I used*:

library (arrayQuality)

targets <- readTargets("targetPMCI.txt")

files <-
c("3a.gpr","3b.gpr","3cDyeSwap.gpr","9bT.gpr","37a.gpr","37b.gpr","37cDyeSwap.gpr","61a.gpr",

"61b.gpr","61cDyeSwap.gpr","75a.gpr","75bT.gpr","75cDyeSwap.gpr","76b.gpr","76cT.gpr","77a.gpr",

"77bT.gpr","77c.gpr","78b.gpr","78cT.gpr","79a.gpr","79b.gpr","79cDYESWAP.gpr","80a.gpr",

"80b.gpr","80cDyeSwap.gpr","81aT.gpr", "81b.gpr","81cDyeSwap.gpr",
"82aT.gpr","82b.gpr","82cDyeSwap.gpr",
"83a.gpr","83b.gpr","83cDyeSwap.gpr","84a.gpr","84b.gpr","84cDyeSwap.gpr","85a.gpr","85b.gpr",

"85cDyeSwap.gpr","86a.gpr","86b.gpr", "86cDyeSwap.gpr","711aT.gpr")

 RG <- read.maimages(files,source="genepix")

 RG$printer <- getLayout(RG$genes)

 RG.b <- backgroundCorrect(RG, method="normexp", offset=50)

library (convert)

RG.Within <- normalizeWithinArrays (RG.b, method="loess")

RG.Between <- normalizeBetweenArrays (RG.Within, method="Aquantile")

genes <- RG.Between$genes
log_ratios <- RG.Between$M
Mean_LogIntensity <- RG.Between$A

Log_Ratio_table <- cbind (genes,log_ratios)
MeanLog_Intensity_table <- cbind (genes,Mean_LogIntensity)

write.csv (Log_Ratio_table,  file="Table of Log-ratio,M (cDNA, PMCI).csv")

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