[BioC] beadarray error messages with BSData function

Mark Cowley m.cowley at garvan.org.au
Wed Oct 27 02:41:36 CEST 2010

Hi Huw,
in R 2.11, the grep function changed & lost the extended argument.
Since you didn't provide sessionInfo() it's impossible to tell which version of R you're running, but you should update your R & Bioconductor to the latest version.

If you still get the error, then your should contact the package maintainer, or try to fix the problem yourself


On 27/10/2010, at 4:01 AM, Huw Jones wrote:

> Hi all,
> No matter how hard I try (or Google) I cannot fix these warning messages (below) that I get repeatedly. I am new to this and have jumped straight in. None of the manuals, or webpages, seem to help.  Can anyone here?? If anyone can, think of it as your good deed for the day!
> Many thanks!
> > BSData <- readBeadSummaryData("C Oikonomou 160708 Project 1 Sample Probe Profile.txt", qcFile="C Oikonomou 160708 Project 1 Control Probe Profile.txt", skip=0, qc.skip=0, controlID="ProbeID")
> Warning messages:
> 1: In grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) :
>  'extended = FALSE' is deprecated
> 2: In grep(colnames(QC[[i]]), colnames(exprs(BSData)), extended = FALSE) :
>  argument 'pattern' has length > 1 and only the first element will be used
> >
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> _______________________________________________
> 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

More information about the Bioconductor mailing list