[BioC] ggTools Error

Tue Jan 19 15:58:02 CET 2010

On Tue, Jan 19, 2010 at 8:11 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Thanks Vincent,
>
> That worked great. I set entrez gene ids as my featureNames() and
> "org.Hs.eg.db" as my annotation platform.
>
> featureNames(ceuExprSet) <- as.character(entrezIds)
> annotation(ceuExprSet) <- "org.Hs.eg.db"
>
> I seems to be working now.
>
> One question, if I run the analysis for all genes across all SNPs (I
> calculate it will take about 2 weeks) does the gwSnpTests() function correct
> for multiple testing? I'm specifically looking for genes related to miRNA

no, there is no multiple testing adjustment in these procedures

> processing so maybe I'd be best to subset on those? Although I'd still be
> interested to see what cropped with the full geneset...
>
> Paul
>
> On Mon, Jan 18, 2010 at 2:37 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>>
>> 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
>> >
>> >
>
>
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
>