Hi Julia, sorry for taking a while for replying, I was away on a conference. Also, replying to the list means that other people can also offer advice and that the conversation will be archived in case other people have this issue. That seems like that the file should be of the proper format from the scanner and the file name. Do all of your files fail, or is there only a specific one that has this issue? Francois On Apr 16, 2010, at 7:19 AM, Turner, Julia wrote: > Hi Francois, > > 1. The scanner is a G2505B. > 2. Here is an example file name: E2F1_251486828858_S01_GE1_107_Sep09_1_3.txt > 3. I was just using setwd("\\\") as an example I am not really setting my working directory to that location:). > > Thanks, > Julia > > -----Original Message----- > From: Francois Pepin [mailto:francois at sus.mcgill.ca] > Sent: Thursday, April 15, 2010 12:52 PM > To: Turner, Julia > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Agi4x44PreProcess_1.6.0 Error in readGenericHeader(fullname, columns = columns, sep = sep) : > > Hi Julia, > > we're going to need a bit more information before we can help you, although we do appreciate the sessionInfo and code snippet. > > Which scanner are you using? Could you give us a few examples of the file names that you are getting from it? > > My guess is that you're not using the same file format as what is expected, although a more obscure bug is also possible. > > Out of curiosity, why are you setting your working directory to '///'? First it should only get you to the root directory (so '/' is enough) and second, it seems like a strange place to put your files. > > Cheers, > > Francois > > On Apr 13, 2010, at 11:04 AM, Turner, Julia wrote: > >> Hi, >> >> I am getting the error , >> >> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >> Specified column headings not found in file >> >> This happens when I try to used the read.AgilentFE function. I have noticed other posts about the limma package, but I believe this is not the same. My session info is: >> >> R version 2.10.1 (2009-12-14) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] mgug4122a.db_2.3.6 org.Mm.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5 Agi4x44PreProcess_1.6.0 >> [6] genefilter_1.28.2 annotate_1.24.1 AnnotationDbi_1.8.2 limma_3.2.3 Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] splines_2.10.1 survival_2.35-7 tools_2.10.1 xtable_1.5-6 >> >> Commands: >>> library(Agi4x44PreProcess) >>> library(mgug4122a.db) >>> setwd("///") >>> targets = read.targets(infile="target_test.txt") >>> dd=read.AgilentFE(targets, makePLOT=FALSE) >> >> Thank you for your time and I apologize if this is posted elsewhere. If it has already been addressed could you please forward me the thread. >> Best, >> Julia >> >> >> >> >> NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.