[BioC] Bug in base.profiles.nc (gcrma)?

[Heidi Dvinge]

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