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Hi, 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. Robert > > I am using a PC running Windows XP, R2.1. > > Thanks - > Tony > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor >

There is no function called 'dir' in the marray package. Note that it is the "marray" package not the "Marray". R is case sensitive. I think the following should suffice fname <- list.files( path=datadir, pattern="\\.spot" ) BTW, dir() is an alias for list.files() and I prefer to use the latter as I think it has a clearer meaning. Regards, Adai On Tue, 2005-07-12 at 16:12 -0500, 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 > > 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. > > I am using a PC running Windows XP, R2.1. > > Thanks - > Tony > > 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor >