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

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 that your version of some package is outdated because your R is  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 outdated (not true in this case).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@...> 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
>
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