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Heike Pospisil
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310
@heike-pospisil-1097
Last seen 10.2 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
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.