[BioC] qc in simpleaffy
Robert Gentleman
rgentlem at fhcrc.org
Tue Apr 28 23:28:07 CEST 2009
Hi Mayte,
Is there some reason not to use arrayQualityMetrics? It gives a much more
comprehensive overview of the quality issues that may be present. simpleaffy's
QC is reasonable, but is very centered on Affymetric suggested methods.
In any event, you are use R 2.8.x and the current releases are 2.9.x, so it
might be good to try to upgrade?
And finally, if it persists, you will have to find a way for someone else to
have access to your data for testing (or show that this happens on one of the
more readily available data sets).
At the very least, perhaps checking the class of qcs to see what was returned
by your call to qc, would be a good start.
thanks
Robert
Mayte Suarez-Farinas wrote:
> Hi all!
>
>
> I try what it was suggested from my previous post. But now I get another
> error:
> I load only the minimum libraries: here is what i got:
>
> library(simpleaffy)
> load("Batch1-AffyBatch.rda")
> qcs<-qc(abatch)
> plot(qcs)
> Error in as.double(y) :
> cannot coerce type 'S4' to vector of type 'double'
>
> so, whats teh problem now??
>
>
>
> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils
> datasets methods base
>
> other attached packages:
> [1] hgu133a2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4
> AnnotationDbi_1.5.18 hgu133plus2cdf_2.3.0
> [6] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1
> genefilter_1.22.0 survival_2.34-1
> [11] affy_1.20.2 Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0
>
>
>
>
> On Apr 23, 2009, at 6:59 PM, Chao-Jen Wong wrote:
>
>> Hi, Mayte,
>>
>> Can you try typing Biobase::annotation(abatch) and see if it still gives
>> any error. If not, then that means the "annotation" method may be
>> crushed by other packages in your search path. It seems to me that you
>> upload a lot of packages into the workspace. Can you try to leave the R
>> environment and call up R again. Don't load too many libraries this
>> time, only affy and simpleaffy and your affyBatch data object. Hope
>> that would work.
>>
>> Chao-Jen
>>
>> Mayte Suarez-Farinas wrote:
>>> Hi everybody:
>>>
>>> I am working with R 2.8 and I the function "qc" from simpleaffy is not
>>> working:
>>>
>>>> q<-qc(abatch)
>>> Error in function (classes, fdef, mtable) :
>>> unable to find an inherited method for function "annotation", for
>>> signature "AffyBatch"
>>>
>>> I get the same error if:
>>>
>>>> annotation(abatch)
>>> Error in function (classes, fdef, mtable) :
>>> unable to find an inherited method for function "annotation", for
>>> signature "AffyBatch"
>>>
>>> but not if:
>>>
>>>> abatch at annotation
>>> [1] "hgu133a2.db"
>>>
>>>
>>> sessionInfo()
>>> R version 2.8.1 (2008-12-22)
>>> i386-apple-darwin8.11.1
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] splines tools stats graphics grDevices utils
>>> datasets methods base
>>>
>>> other attached packages:
>>> [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0
>>> Harshlight_1.12.0 altcdfenvs_2.4.0
>>> [5] hypergraph_1.14.0 Biostrings_2.10.16
>>> IRanges_1.0.12 makecdfenv_1.20.0
>>> [9] affyio_1.10.1 beadarray_1.10.0
>>> sma_0.5.15 hwriter_1.0
>>> [13] affycoretools_1.14.1 annaffy_1.14.0
>>> KEGG.db_2.2.5 biomaRt_1.16.0
>>> [17] GOstats_2.8.0 Category_2.8.4
>>> RBGL_1.18.0 GO.db_2.2.5
>>> [21] RSQLite_0.7-1 DBI_0.2-4
>>> graph_1.20.0 limma_2.16.4
>>> [25] affyQCReport_1.20.0 geneplotter_1.20.0
>>> annotate_1.20.1 AnnotationDbi_1.5.18
>>> [29] lattice_0.17-17 RColorBrewer_1.0-2
>>> affyPLM_1.18.1 preprocessCore_1.4.0
>>> [33] xtable_1.5-4 simpleaffy_2.18.0
>>> gcrma_2.14.1 matchprobes_1.14.1
>>> [37] genefilter_1.22.0 survival_2.34-1
>>> affy_1.20.2 Biobase_2.2.2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21
>>> RCurl_0.94-1 XML_2.1-0
>>> [6] cluster_1.11.11 grid_2.8.1
>>>
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>>
>>
>> --
>> Chao-Jen Wong
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Avenue N., M2-B876
>> PO Box 19024
>> Seattle, WA 98109
>> 206.667.4485
>> cwon2 at fhcrc.org
>>
>
> _______________________________________________
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>
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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