[BioC] A question about the Marray Package
rgentlem at fhcrc.org
Wed Jul 13 17:00:19 CEST 2005
Tony Kowal wrote:
> Hi All,
> I am trying to read in microarray data from a two-color platform using the Marray package. One of
> the commands that I have used to read in data (with R 2.0 and R2.01) is not working for me with
> R2.1. I was wondering if anyone has encountered this problem, and can tell me how to fix the
> problem. Thanks very much in advance for your help.
> I use the "fnames" command to specify that I wish to read in a SPOT file:
>>fnames <- dir(path = datadir, pattern = paste("*", "spot", sep = "."))
> and I receive the following error message:
> Error in list.files(path, pattern, all.files, full.names, recursive) :
> invalid 'pattern' regular expression
Which means just what it says. What you used is not a valid regular
expression and while it did work for a while it was not valid. R fixed
its regular expression handling - and some things like this have stopped
working (but they should never have worked in the first place).
paste(".*", "spot", sep=".")
is probably what you intended in the first place, but you might want
to look at a reference on regular expressions to be sure.
> As I mentioned, the fnames command as I typed above has worked in earlier versions of R, but seems
> to be a problem with R2.1.
the output of sessionInfo would be of much more help here.
> I am using a PC running Windows XP, R2.1.
> Thanks -
> Tony Kowal
> Graduate Student
> Rex Chisholm Laboratory
> Northwestern University
> 303 E. Superior
> Lurie Building
> Room 7-250
> Chicago, IL 60611
> Lab: 312 503 4169
> e-mail: askowal at northwestern.edu
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor