[BioC] dye-swap and arrayMagic

[Andreas Buness]

Hallo Balazs,

## you could do the following:
##############################

yourDataObject <- resultList$exprSetRG

logRatios <- getExprSetLogRatio(yourDataObject)

nrOfSlides <- dim(exprs(logRatios))[2]
odd <- seq(1, nrOfSlides, by=2)

exprs(logRatios)[,odd] <- (-1) * exprs(logRatios)[,odd]

exprs2excel(logRatios)

## or alternatively, when using writeToFile:
############################################

greenOdd <- getIndGreen(yourDataObject)[odd]
redOdd   <- getIndRed(yourDataObject)[odd]
bothOdd <- c(greenOdd, redOdd)

exprs(yourDataObject)[,bothOdd] <- (-1) * exprs(yourDataObject)[,bothOdd]

writeToFile(resultList$arrayDataObject, yourDataObject)



Best Regards
Andreas

Dr_Gyorffy_Balazs wrote:
> Hallo everyone!
> 
> I have analysed 108 Genepix arrays using the arrayMagic
> package. However, I have a problem: every second array is a
> repetition of the previous array with dye-swap (normal: 1,
> 3, 5, ... dye-swap: 2, 4, 6, ...). How can I correct the
> logratios output (the writeToFile function) in order to get
> the correct values for the dye-swapped chips?
> 
> Thank
> Balazs Györffy
> 
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