Hi Tony, no svn I'm afraid. If you could do that for me that'd be great. And yes, I know I ought to jump to R-2.8 - it's slowly but steadily climbing up on my to-do list ;) Cheers \Heidi On 16 May 2008, at 19:09, Tony Chiang wrote: > 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 that your version of some package is outdated because your R is 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 outdated (not true in this case).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@ebi.ac.uk> 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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]