Hi, Can anybody help me with this? 1) I've downloaded from the ArrayExpress some GenePix files that don't have headers. Because of that I had to read the files (.txt extension for some reason) this way: RG <- read.maimages(targets$Filename, columns=list(Rf="GenePix:F635 Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635 Median",Gb="GenePix:B532 Median"), sep="\t", path="./") Is this correct? 2) I had to create the targets files from a file provided by arrayexpress which looked something like this: SlideNumber Source Name Label FileName 1 8CT Cy5 1348628744.txt 2 5Exp Cy3 1348628729.txt 3 10Exp Cy5 1348628754.txt 4 4CT Cy3 1348628724.txt 5 1Exp Cy5 1348628709.txt 6 12Exp Cy5 1348628764.txt 7 6Exp Cy5 1348628734.txt 8 3CT Cy3 1348628719.txt 9 13Exp Cy3 1348628769.txt 10 7Exp Cy3 1348628739.txt 11 2CT Cy5 1348628714.txt 12 11Exp Cy3 1348628759.txt 13 9Exp Cy5 1348628749.txt 14 14CT Cy3 1348628774.txt And my target file looks like this SlideNumber Filename Cy3 Cy5 1 1348628744.txt case control 2 1348628729.txt case control 3 1348628754.txt control case 4 1348628724.txt control case 5 1348628709.txt control case 6 1348628764.txt control case 7 1348628734.txt control case 8 1348628719.txt control case 9 1348628769.txt case control 10 1348628739.txt case control 11 1348628714.txt case control 12 1348628759.txt case control 13 1348628749.txt control case 14 1348628774.txt control case Is this correct? Luana _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. rial_Storage_062009 [[alternative HTML version deleted]]

Hi Juan If you look at the code for read.maimages there appear to be four entries for genepix: genepix = , (Not sure what this does). genepix.mean = list(R = "F635 Mean", G = "F532 Mean", Rb = "B635 Median", Gb = "B532 Median"), genepix.median = list(R = "F635 Median", G = "F532 Median", Rb = "B635 Median", Gb = "B532 Median"), genepix.custom = list(R = "F635 Mean", G = "F532 Mean", Rb = "B635", Gb = "B532"), Your code columns are Rf="GenePix:F635Mean", Gf="GenePix:F532 Mean", Rb="GenePix:B635 Median", Gb="GenePix:B532 Median") which nearly match the genepix.mean entry. (I don't think you need the "GenePix:" in each entry. Also perhaps "R" and "G", not "Rf", and "Gf"). Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Juana Arco Sent: 23 June 2009 14:53 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Limma - GenePix Hi, Can anybody help me with this? 1) I've downloaded from the ArrayExpress some GenePix files that don't have headers. Because of that I had to read the files (.txt extension for some reason) this way: RG <- read.maimages(targets$Filename, columns=list(Rf="GenePix:F635 Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635 Median",Gb="GenePix:B532 Median"), sep="\t", path="./") Is this correct? 2) I had to create the targets files from a file provided by arrayexpress which looked something like this: SlideNumber Source Name Label FileName 1 8CT Cy5 1348628744.txt 2 5Exp Cy3 1348628729.txt 3 10Exp Cy5 1348628754.txt 4 4CT Cy3 1348628724.txt 5 1Exp Cy5 1348628709.txt 6 12Exp Cy5 1348628764.txt 7 6Exp Cy5 1348628734.txt 8 3CT Cy3 1348628719.txt 9 13Exp Cy3 1348628769.txt 10 7Exp Cy3 1348628739.txt 11 2CT Cy5 1348628714.txt 12 11Exp Cy3 1348628759.txt 13 9Exp Cy5 1348628749.txt 14 14CT Cy3 1348628774.txt And my target file looks like this SlideNumber Filename Cy3 Cy5 1 1348628744.txt case control 2 1348628729.txt case control 3 1348628754.txt control case 4 1348628724.txt control case 5 1348628709.txt control case 6 1348628764.txt control case 7 1348628734.txt control case 8 1348628719.txt control case 9 1348628769.txt case control 10 1348628739.txt case control 11 1348628714.txt case control 12 1348628759.txt case control 13 1348628749.txt control case 14 1348628774.txt control case Is this correct? Luana _________________________________________________________________ Hotmail(r) has ever-growing storage! Don't worry about storage limits. rial_Storage_062009 [[alternative HTML version deleted]]

Hi Juana Having read your email more closely perhaps what I sent you is not useful. Unless there is some feature of limma I do not know about I do not think what you are doing can work. I think read.maimages needs the header names at some point, so if you have not got them you will have to supply them. Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Juana Arco Sent: 23 June 2009 14:53 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Limma - GenePix Hi, Can anybody help me with this? 1) I've downloaded from the ArrayExpress some GenePix files that don't have headers. Because of that I had to read the files (.txt extension for some reason) this way: RG <- read.maimages(targets$Filename, columns=list(Rf="GenePix:F635 Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635 Median",Gb="GenePix:B532 Median"), sep="\t", path="./") Is this correct? 2) I had to create the targets files from a file provided by arrayexpress which looked something like this: SlideNumber Source Name Label FileName 1 8CT Cy5 1348628744.txt 2 5Exp Cy3 1348628729.txt 3 10Exp Cy5 1348628754.txt 4 4CT Cy3 1348628724.txt 5 1Exp Cy5 1348628709.txt 6 12Exp Cy5 1348628764.txt 7 6Exp Cy5 1348628734.txt 8 3CT Cy3 1348628719.txt 9 13Exp Cy3 1348628769.txt 10 7Exp Cy3 1348628739.txt 11 2CT Cy5 1348628714.txt 12 11Exp Cy3 1348628759.txt 13 9Exp Cy5 1348628749.txt 14 14CT Cy3 1348628774.txt And my target file looks like this SlideNumber Filename Cy3 Cy5 1 1348628744.txt case control 2 1348628729.txt case control 3 1348628754.txt control case 4 1348628724.txt control case 5 1348628709.txt control case 6 1348628764.txt control case 7 1348628734.txt control case 8 1348628719.txt control case 9 1348628769.txt case control 10 1348628739.txt case control 11 1348628714.txt case control 12 1348628759.txt case control 13 1348628749.txt control case 14 1348628774.txt control case Is this correct? Luana _________________________________________________________________ Hotmail(r) has ever-growing storage! Don't worry about storage limits. rial_Storage_062009 [[alternative HTML version deleted]]