Dear Hua, Further to Kasper's post, you may find the following informative: for (a in files) cat(a,readGPRHeader(a)$Wavelengths,"\n") Best wishes Gordon >Hua Weng hweng at biochem.okstate.edu >Tue Dec 6 21:16:04 CET 2005 [snip] >The following is the header part of my gpr file: > >ATF 1 >27 82 >Type=GenePix Results 2 >DateTime=2005/10/01 20:10:53 >Settings=D:\USERS\DeSilva\asitha\GAL Files\good >gals_3Plates_3X2reps\Hyb4_brahma_6hours_01oct05.gps >GalFile=D:\USERS\DeSilva\asitha\GAL Files\good >gals_3Plates_3X2reps\3_plates_2x3_reps_4x4_pins_printed083005_Modnew7 .gal > >PixelSize=10 >"Wavelengths=650 546" [snip] > And the following is the error message from the command: >> library(limma) >> files <- dir(pattern=".gpr") >> RG <- read.maimages(files, columns=list(R="F532 Mean", G="F635 >> Mean", Rb="B532 Median", Gb="B635 Median"), wt.fun=wtflags(0.1)) > Error in switch(source2, quantarray = { : Cannot find column > heading in image output file

Dear Kasper and Gordon: Thank you very much for all the suggestions. I'm going to debug my data files to see whether there is something been messed up. Best Regards, Hua -----Original Message----- From: Gordon Smyth [mailto:smyth@wehi.edu.au] Sent: Tuesday, December 06, 2005 11:44 PM To: Hua Weng Cc: BioC Mailing List; Kasper Daniel Hansen Subject: [BioC] Error message from R2.2.0 on Linux Dear Hua, Further to Kasper's post, you may find the following informative: for (a in files) cat(a,readGPRHeader(a)$Wavelengths,"\n") Best wishes Gordon >Hua Weng hweng at biochem.okstate.edu >Tue Dec 6 21:16:04 CET 2005 [snip] >The following is the header part of my gpr file: > >ATF 1 >27 82 >Type=GenePix Results 2 >DateTime=2005/10/01 20:10:53 >Settings=D:\USERS\DeSilva\asitha\GAL Files\good >gals_3Plates_3X2reps\Hyb4_brahma_6hours_01oct05.gps >GalFile=D:\USERS\DeSilva\asitha\GAL Files\good >gals_3Plates_3X2reps\3_plates_2x3_reps_4x4_pins_printed083005_Modnew7 .gal > >PixelSize=10 >"Wavelengths=650 546" [snip] > And the following is the error message from the command: >> library(limma) >> files <- dir(pattern=".gpr") >> RG <- read.maimages(files, columns=list(R="F532 Mean", G="F635 >> Mean", Rb="B532 Median", Gb="B635 Median"), wt.fun=wtflags(0.1)) > Error in switch(source2, quantarray = { : Cannot find column > heading in image output file