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 Gy?rffy

The dye-swap columns need to be multiplied by -1 if they are log ratios -----Original Message----- From: Dr_Gyorffy_Balazs [mailto:zsalab2@yahoo.com] Sent: 06 July 2004 10:35 To: bioconductor@stat.math.ethz.ch Subject: [BioC] dye-swap and arrayMagic 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 Gy?rffy _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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 Gy?rffy > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor