I get the error \"Error in readGenericHeader(fullname, columns = columns) : Specified column headings not found in file In addition: Warning message: In file(file, \"r\") : file(\"\") only supports open = \"w+\" and open = \"w+b\": using the former\" when I use RG <- read.maimages(targets$FileName, source=\"agilent\", annotation= c(\"FeatureNum\", \"Row\", \"Col\",\"ProbeUID\", \"ControlType\",\"ProbeName\", \"GeneName\", \"SystematicName\")). Then I used RG <- read.maimages(targets, source=\"agilent\"), I got the same error as the former one, which is Error is readGenericHeader(fullname, columns = columns) : Specified column headings not found in file In addition: Warning message: In file(file, \"r\") : file(\"\") only supports open = \"w+\" and open = \"w+b\": using the former Thanks for your help! Kathy -- output of sessionInfo(): readGenericHeader(fullname, columns = columns) : Specified column headings not found in file In addition: Warning message: In file(file, \"r\") : file(\"\") only supports open = \"w+\" and open = \"w+b\": using the former -- Sent via the guest posting facility at bioconductor.org.

Dear Kathy, try to use quote sign without escape character, i.e. " not \" . Limma doesn't require escape character. Also, as target you can specify file as simply "targets", if it has "FileName" column it will be read automatically. HTH Maciej > Subject: [BioC] read.maimage error message > Message: 4 > MIME-Version: 1.0 > > > I get the error \"Error in readGenericHeader(fullname, columns = > columns) : > Specified column headings not found in file > In addition: Warning message: > In file(file, \"r\") : > file(\"\") only supports open = \"w+\" and open = \"w+b\":using the > former\" when I use RG <- read.maimages(targets$FileName, source=\"agilent\", annotation= c(\"FeatureNum\", \"Row\", \"Col\",\"ProbeUID\", \"ControlType\",\"ProbeName\", \"GeneName\", \"SystematicName\")). > Then I used RG <- read.maimages(targets, source=\"agilent\"), I got > the same error as the former one, which is Error is > readGenericHeader(fullname, columns = columns) : > Specified column headings not found in file > In addition: Warning message: > In file(file, \"r\") : > file(\"\") only supports open = \"w+\" and open = \"w+b\": using > the former > > Thanks for your help! > > Kathy > > -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com