Hello everyone, first of all, I'd like to wish Chanukah Sameach and Merry Christmas! I wrote a few day ago because I was haveing problems in reading my targets.txt file with the Limma package. This problem was solved (thanks Jim). Now, I'm having problems with the read.maimages command. I used the ScanArray Express software to generate my files. I have a .csv and a .gpr file. My Targets.txt file is: SlideNumber Name FileName Cy3 Cy5 Date 1 83 N1 CLB_Cy3_CL14_Cy5_13860883_18Dez2008.gpr CLB CL14 2008/18/12 2 85 N2 CL14_Cy3_CLB_Cy5_13860885_18Dez2008.gpr CL14 CLB 2008/18/12 The commands that I tryied were: RG <- read.maimages(targets$FileName, source="genepix") Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected RG <- read.maimages(targets$FileName, source="genepix", sep="\t") Erro em `[.data.frame`(obj, , columns[[a]]) : undefined columns selected Any suggestions? Thanks very much! Priscila -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]

I tried something new: RG <- read.maimages(targets$FileName, source="scanarrayexpress") Erro em readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file Thanks again, Priscila [[alternative HTML version deleted]]

On Mon, Dec 22, 2008 at 10:48:50AM -0200, Priscila Grynberg wrote: > ScanArray Express software to generate my files. I have a .csv and a .gpr > file. > > My Targets.txt file is: > > SlideNumber Name FileName Cy3 Cy5 > Date > 1 83 N1 CLB_Cy3_CL14_Cy5_13860883_18Dez2008.gpr CLB CL14 > 2008/18/12 > 2 85 N2 CL14_Cy3_CLB_Cy5_13860885_18Dez2008.gpr CL14 CLB > 2008/18/12 > > The commands that I tryied were: > > RG <- read.maimages(targets$FileName, source="genepix") > Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected > > RG <- read.maimages(targets$FileName, source="genepix", sep="\t") > Erro em `[.data.frame`(obj, , columns[[a]]) : undefined columns selected > RG <- read.maimages(targets$FileName, source="scanarrayexpress") > Erro em readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file Are these copy&pasted? I'm asking, because the messages are not the same and contain spelling errors. Anyway, the messages suggest that your gpr files do not contain the column headings expected. According to the source code of read.maimages, the expected columns for source 'scanarrayexpress' are: G = "Ch1 Mean", Gb = "Ch1 B Median", R = "Ch2 Mean", Rb = "Ch2 B Median" Have a look at your files and make sure these columns are present. If they are not, you have to specify the columns to be used yourself using source='generic' and the columns option. See ?read.maimages for details. cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel