Hi Wolfgang, Thanks for pointing me out to the right direction. After looking at TargetInfo at maInfo, I realized that there were three extra lines in the TargetMSS.txt file. That is why I was getting an error message. Thanks again, Best, Mete Quoting mete at seas.upenn.edu: > Hi Wolfgang, > > Here is the answer: > >> target.info at maInfo$Filename > NULL > > Thanks so much for your help. > > Mete > > Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > >> >> Mete, >> >> what is the complete set of 111 values of TargetInfo at maInfo$Filename? >> >> Best wishes >> Wolfgang >> >> mete at seas.upenn.edu ha scritto: >>> Hi Wolfgang, >>> >>> Thanks for your quick reply. To answer your questions. TargetInfo is >>> >>>> TargetInfo >>> An object of class "marrayInfo" >>> @maLabels >>> [1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt" >>> 111 more elements ... >>> >>> @maInfo >>> FileName SampleID HybridizationSeq Cy3 Cy5 HybDate >>> 1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006 >>> 2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006 >>> 3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006 >>> 4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006 >>> 5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006 >>> 111 more rows ... >>> >>> @maNotes >>> [1] "TargetMSS.txt" >>> >>> and sessionInfo is: >>> >>>> sessionInfo() >>> R version 2.5.1 (2007-06-27) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] "grid" "tools" "tcltk" "stats" "graphics" "grDevices" >>> [7] "utils" "datasets" "methods" "base" >>> >>> other attached packages: >>> arrayQuality RColorBrewer gridBase hexbin lattice >>> convert >>> "1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" >>> "1.10.0" >>> marray tkWidgets DynDoc Biobase widgetTools >>> limma >>> "1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" >>> "2.9.17" >>> >>> >>> >>> Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: >>> >>>> Dear Mete, >>>> >>>> what is the value of your Variable "TargetInfo"? Does it contain empty >>>> strings? Also, what is the output of sessionInfo()? >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> @seas.upenn.edu ha scritto: >>>>> Dear All, >>>>> >>>>> I get an error message after executing the following commands on RGUI >>>>> >>>>>> library(arrayQuality) >>>>>> library(marray) >>>>>> TargetInfo<-read.marrayInfo("TargetMSS.txt") >>>>>> mraw<-read.Agilent(targets=TargetInfo) >>>>> >>>>> >>>>> I get the following: >>>>> >>>>> Reading ... ./RCP6NEW.txt >>>>> Reading ... ./RCP7NEW.txt >>>>> Reading ... ./RCP8NEW.txt >>>>> Reading ... ./ >>>>> Error in file(file, "r") : unable to open connection >>>>> In addition: Warning message: >>>>> cannot open file './', reason 'Permission denied' in: file(file, "r") >>>>> >>>>> The working directory is correct and I do have an active internet >>>>> connection. I am not sure why I am getting this warning >>>>> message. Any comments will be appreciated. >>>>> >>>>> Best, >>>>> >>>>> Mete Civelek >>>>> >>> >>> >> >> >> -- >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > _______________________________________________ > 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 >