Hi,

I wish to use R to have the log(2) expressions of genes from a few cDNA
samples (from layout: PMCI_10.5KSC_GP.gal). The experiment is done with a
common reference, and dye swaps are carried out for different wild types
too; for example:



WildType A

Test

ref

WildType A

Ref

Test

Wild type B

Test

Ref

Wild type B

Test

Ref

Wild type B

ref

test

...........

......

.....











For this, although I was trying the following commands, but was unsure as to
where and how I would integrate the above information. Also, I am not very
sure and thus, please suggest how I can finally obtain the log2-expression
values!

Hope you would kindly reply.

Thank you !

Cheers,

Santana

= = === = = = = = ==  =

library(arrayQuality)

 targets <- readTargets("target.txt")

 files <- c("##.gpr", " ##.gpr" ..........)  # file names are not written
down

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

RG$printer <- getLayout(RG$genes)

RG.b <- backgroundCorrect(RG, method="none")

library (convert)

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

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

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)

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