[BioC] ggTools Error

[Vincent Carey]

The best possible explanation is that gs1 includes a probe set id that
is not present in exprs(hapSmlSet)
get(pname) is attempting to retrieve the expression values for probes
enumerated in gs1

i am sorry that the error message is cryptic; this package is
undergoing renovation to improve performance
and user interface.  continue to post your concerns to the list; don't
forget sessionInfo()

On Fri, Jan 15, 2010 at 8:37 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Hi List,
>
> I'm trying to run an association analysis with GGTools. I'm getting an error
> when I run:
>
>> outData <- gwSnpTests(gs1~male, hapSmlSet)
> Error in data.frame(get(pname), pData(sms)) :
> arguments imply differing number of rows: 0, 87
>
> There are 87 samples in my analysis so that explains that, but I don't know
> what "get(pname)" is doing or why it is returning 0. I'm guessing I've
> something missing somewhere in the data I've loaded.
>
> I can provide more information if necessary.
>
> Thanks,
>
> Paul
>
>
>
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_IE.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_IE.UTF-8        LC_COLLATE=en_IE.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_IE.UTF-8
>  [7] LC_PAPER=en_IE.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] org.Hs.eg.db_2.3.6  GGtools_3.4.0       rpart_3.1-46
>  [4] Biostrings_2.14.0   IRanges_1.4.0       RColorBrewer_1.0-2
>  [7] GGBase_3.6.0        RSQLite_0.8-0       DBI_0.2-5
> [10] snpMatrix_1.10.3    survival_2.35-8     GSEABase_1.8.0
> [13] graph_1.24.1        annotate_1.24.0     AnnotationDbi_1.8.0
> [16] GEOquery_2.10.0     RCurl_1.3-0         bitops_1.0-4.1
> [19] Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] annaffy_1.18.0 tcltk_2.10.1   tools_2.10.1   XML_2.6-0
> xtable_1.5-6
>>
>
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
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>
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