[BioC] ggTools Error

Mon Jan 18 15:37:53 CET 2010

Thanks for additional info; let's keep this on the list.  It turns out
that this use case is not covered by current code.  The most common
expression featureNames in applications are array probe(set)
identifiers.  gwSnpTests handles the situation where the GeneSet for
the response has "biologically oriented" identifiers like HUGO symbols
(so a relevant GeneSet would have geneIdType SymbolIdentifier()), but
the expression data rows are labeled with annotation-oriented
identifiers (with geneIdType AnnotationIdentifier([platform
specification]).

Because we don't have formal types for featureNames output (we just
get character strings) it is hard for me to check for this situation.
I will think about a way out that handles your use case; for now, if
you could map your expression featureNames to those of some relevant
annotated platform, you could go forward with the same call upon
setting the annotation slot of the smlSet appropriately.  In
particular if you wanted to use Entrez IDs, it should work to use
org.[something].eg.db for the annotation (assuming you did not use
some bioc-annotated microarray platform to get your expression data)
but I have not tried this.

On Mon, Jan 18, 2010 at 7:32 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Hi Vincent,
>
> Thanks for your reply. It doesn't look to me like that's the problem though.
> I've pasted some code/output below. Is there anything else that springs to
> mind? It'd be great if I could get this working:
>
>> exprs(hapSmlSet)[1:5, 1:5]
>          NA06985  NA07048  NA07055  NA07056  NA07345
> TTLL10  5.804398 6.111066 6.015460 6.077223 6.052570
> B3GALT6 6.900609 6.614555 6.770701 6.688613 6.570467
> SCNN1D  5.698484 6.148147 5.777978 5.892331 6.073576
> PUSL1   7.010970 6.970204 7.045875 7.424906 6.785346
> VWA1    6.559377 6.689263 6.447208 6.574919 5.988598
>
>> gs1 = GeneSet(c("TTLL10", "VWA1"))
>> geneIdType(gs1) = SymbolIdentifier()
>>
>>
>> outData <- gwSnpTests(gs1~male, hapSmlSet)
> Error in data.frame(get(pname), pData(sms)) :
>   arguments imply differing number of rows: 0, 87
>>
>
>
> Thanks,
>
> Paul.
>
>
>
> On Fri, Jan 15, 2010 at 3:36 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>>
>> 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
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>> >
>
>
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
>