Re: Bug in base.profiles.nc (gcrma)?

Hi Heidi,

It certainly looks like you found a bug. And I think this has not been fixed
because I just had a peek at the source file. Can you send a note to the
maintainer with your patch? That is can you download the source file via
svn, change the code and then send the maintainer the output of svn diff? If
you don't have svn, let me know and I can do this for you.

It might also be a good idea to update your R since the stable version of R
2.7.0 was released a few weeks ago, and someone might yell at you about
updating your R because there can be instances that your version of some
package is outdated because your R is outdated (not true in this case).

Cheers,
--tony

On Fri, May 16, 2008 at 6:48 PM, Heidi Dvinge <heidi@...> wrote:

> Hi,
>
> I'm trying to use gcrma with affinity.source= "local", and a predefined
> set of NCprobes with gcrma v. 2.12.0. However, I'm running into problems
> with the sub-function base.profiles.nc. I think that where it says:
>
>    if (length(seqs) < length(NCprobe)) {
>        cat("\nNote: some of your negative control probes do not have
> sequence information\n")
>        subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename),
>            xy2indices(p$x, p$y + 1), cdf = cdfpackagename),
>            NCprobe)
>        subIndex2 <- subIndex2[!is.na(subIndex2)]
>        bgy <- bgy[!is.na(subIndex1), ]
>    }
>
> isn't is supposed to be:
>
>    if (length(seqs) < length(NCprobe)) {
>        cat("\nNote: some of your negative control probes do not have
> sequence information\n")
>        subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename),
>            xy2indices(p$x, p$y + 1, cdf = cdfpackagename)),       #
> moving the ")" here
>            NCprobe)
>        subIndex2 <- subIndex2[!is.na(subIndex2)]
>        bgy <- bgy[!is.na(subIndex1), ]
>    }
>
> Thanks
> \Heidi
>
> > sessionInfo()
> R version 2.7.0 Under development (unstable) (2008-02-12 r44439)
> i386-apple-darwin8.10.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
>  [1] mogene10stv1probe_0.0.1    biomaRt_1.13.10            RCurl_0.8-3
>  [4] arrayQualityMetrics_1.4.18 beadarray_1.7.3
>  latticeExtra_0.3-1
>  [7] simpleaffy_2.15.02         affyPLM_1.15.5
> RColorBrewer_1.0-2
> [10] genefilter_1.17.12         survival_2.34
> mogene10stv1cdf_1.18.0
> [13] geneplotter_1.17.7         annotate_1.17.12           xtable_1.5-2
> [16] AnnotationDbi_1.2.0        RSQLite_0.6-7              DBI_0.2-4
> [19] gcrma_2.12.0               matchprobes_1.11.0         vsn_3.4.13
> [22] limma_2.13.4               lattice_0.17-4             affy_1.17.3
> [25] preprocessCore_1.1.5       affyio_1.7.17              Biobase_1.99.4
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-22 XML_1.93-2
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@...
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor