marray: problems loading genepix-files
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@heike-pospisil-1097
Last seen 8.4 years ago
Hello again, as already mentioned in the thread 'Help with GenePix files' the import of my genepix files using the marray package failed. With this post, I am sending the output of sessionInfo() and traceback() just after getting the error message. Thanks a lot for any suggestion and best wishes, Heike ################################################################# > myTargetsa <- read.marrayInfo(file.path(data.dir, "targeta.txt")) > galinfo<-read.Galfile("3kArray5.gal") > data<-read.GenePix(c("a.gpr","ar.gpr"),targets=myTargetsa,layout=galin fo$layout,gnames=galinfo$gnames,) Reading ... a.gpr Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed ################################################################# > traceback() 4: read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote, check.names = FALSE, as.is = TRUE, comment.char = "", nrows = nspots, ...) 3: read.marrayRaw(fnames = c("a.gpr", "ar.gpr"), name.Gf = "F532 Median", name.Gb = "B532 Median", name.Rf = "F635 Median", name.Rb = "B635 Median", name.W = "Flags", layout = <s4 object="" of="" class="" "marraylayout"="">, gnames = <s4 object="" of="" class="" "marrayinfo"="">, targets = <s4 object="" of="" class="" "marrayinfo"="">, notes = "GenePix Data", sep = "\t", quote = "\"", DEBUG = FALSE, path = NULL, skip = NULL, fill = TRUE) 2: do.call("read.marrayRaw", maRaw.args) 1: read.GenePix(c("a.gpr", "ar.gpr"), targets = myTargetsa, layout = galinfo$layout, gnames = galinfo$gnames, ) ################################################################# > sessionInfo() R version 2.4.1 (2006-12-18) i686-pc-linux-gnu locale: LC_CTYPE=en_US.ISO-8859-1;LC_NUMERIC=C;LC_TIME=en_US.ISO-8859-1;LC_COL LATE=en_US.ISO-8859-1;LC_MONETARY=en_US.ISO-8859-1;LC_MESSAGES=en_US.I SO-8859-1;LC_PAPER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHON E=C;LC_MEASUREMENT=en_US.ISO-8859-1;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: marray limma "1.12.0" "2.8.1" -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312
marray marray • 1.2k views
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FYI I got this same error 13.5 years later. You may need to skip the lines until you reach the headers. Genepix files have many lines before header. Also @Jean Yee Hwa Yang, we might want to update documentation and add a note about this in the documentation. Even though function default is 'skip=NULL' it's not intuitive that it calls read.table and there is nothing about this in the documentation and so it's assumed marray takes care of this similar to how GEOquery::getGEO takes care of parsing the rma series files from the GEO database.

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@jean-yee-hwa-yang-1628
Last seen 8.4 years ago
Hi Heike I am guessing there is a mismatch between the gal file and the gpr file you are reading in. Usually the first 5 columns of any gpr file is the same as the gal file. Please try the two options and let me know how you go Option 1 data = read.GenePix(fnames = c("a.gpr", "ar.gpr")) Option 2 myTargetsa <- read.marrayInfo(file.path(data.dir, "targeta.txt")) data = read.GenePix(targets = myTargetsa) Please also show me myTargetsa. If you have further problems, you are welcome to send me a link where I can download your gpr file and take a look. Cheers Jean > ################################################################# > > myTargetsa <- read.marrayInfo(file.path(data.dir, "targeta.txt")) > > galinfo<-read.Galfile("3kArray5.gal") > > > data<-read.GenePix(c("a.gpr","ar.gpr"),targets=myTargetsa,layout=gal info$layout,gnames=galinfo$gnames,) > > Reading ... a.gpr > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > ################################################################# > > traceback() > 4: read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote, > check.names = FALSE, as.is = TRUE, comment.char = "", nrows = > nspots, > ...) > 3: read.marrayRaw(fnames = c("a.gpr", "ar.gpr"), name.Gf = "F532 Median", > name.Gb = "B532 Median", name.Rf = "F635 Median", name.Rb = > "B635 Median", > name.W = "Flags", layout = <s4 object="" of="" class="" "marraylayout"="">, > gnames = <s4 object="" of="" class="" "marrayinfo"="">, targets = <s4 object=""> of class "marrayInfo">, > notes = "GenePix Data", sep = "\t", quote = "\"", DEBUG = FALSE, > path = NULL, skip = NULL, fill = TRUE) > 2: do.call("read.marrayRaw", maRaw.args) > 1: read.GenePix(c("a.gpr", "ar.gpr"), targets = myTargetsa, layout = > galinfo$layout, > gnames = galinfo$gnames, ) > #################################################################
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