[BioC] problems with Affymetrix probes id using exonmap and xmapcore

Sun May 1 12:22:16 CEST 2011

Hi again

Sorry for the late responses, it's a big public holiday here in the UK...

Can you give an example of the code which is returning NULL?

Cheers,

Tim

On 28/04/2011 16:05, "Gomez Moruno, Antonio" <agomezm at idibell.cat> wrote:

> Hi Tim,
> 
> the problem is that i need to process the data previously with exonmap and
> then try to annotate this data with xmapcore. Could it be possible? >From your
> reply i assume that i can normalize the data and work with probesets using
> only xmapcore?? But, i read the doc concerning xmapcore and  i didn't find
> nothing about it.
> 
> I tried to use another Affymetrix related package, oligo, and i obtained this
> info about my data
> 
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 257430 features, 12 samples
>   element names: exprs
> protocolData
>   rowNames: IG100120JMI035-3gst_01.CEL IG100120JMI036-3gst_01.CEL ...
>     IG100120JMI046-3gst_01.CEL (12 total)
>   varLabels: exprs dates
>   varMetadata: labelDescription channel
> phenoData
>   rowNames: IG100120JMI035-3gst_01.CEL IG100120JMI036-3gst_01.CEL ...
>     IG100120JMI046-3gst_01.CEL (12 total)
>   varLabels: index
>   varMetadata: labelDescription channel
> featureData
>   featureNames: 7892501 7892502 ... 8180418 (257430 total)
>   fvarLabels: probesetid seqname ... probesettype (39 total)
>   fvarMetadata: labelDescription
> experimentData: use 'experimentData(object)'
> Annotation: pd.hugene.1.0.st.v1
> 
> So, the numbers that i got here are the same that i got in exonmpa, how can i
> handle this on xmapcore??
> 
> Thanks 
> 
> ________________________________________
> De: Tim Yates [TYates at picr.man.ac.uk]
> Enviat el: dijous, 28 / abril / 2011 15:20
> Per a: Gomez Moruno, Antonio
> Tema: Re: [BioC] problems with Affymetrix probes id using exonmap and xmapcore
> 
> Hiya,
> 
> You seem to have both the deprecated exonmap package, and the xmapcore package
> loaded at the same time.
> 
> This will cause misbehavior at best, and crashes at worst.
> 
> Can you try with just xmapcore loaded, and if that still doesn't work, can you
> post a failing example of your code?
> 
> Cheers,
> 
> Tim
> 
> 
> 
> ----- Reply message -----
> From: "Gomez Moruno, Antonio" <agomezm at idibell.cat>
> Date: Thu, Apr 28, 2011 08:58
> Subject: [BioC] problems with Affymetrix probes id using exonmap and xmapcore
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> 
> I got several .CEL files to do RMA using exonmap library, when i got my list
> significant differentially expressed probesets and i try to use xmapcore to
> map to annotation using "exonic", all i got is a NULL vector. I used xmapcore
> examples and all worked perfectly, but my list of Probesets have no
> correspondance in xmapcore. Anyone has any idea?
> 
> This is my session info
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] hugene10stv1cdf_2.8.0                hugene10sttranscriptcluster.db_7.0.1
>  [3] hugene10stprobeset.db_7.0.1          org.Hs.eg.db_2.5.0
>  [5] RSQLite_0.9-4                        AnnotationDbi_1.14.1
>  [7] limma_3.8.1                          plier_1.22.0
>  [9] exon.pmcdf_1.1                       xmapcore_1.6.0
> [11] IRanges_1.10.0                       RMySQL_0.7-5
> [13] DBI_0.2-5                            RColorBrewer_1.0-2
> [15] genefilter_1.34.0                    affy_1.30.0
> [17] Biobase_2.12.1                      exonmap_2.0.03
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.20.0         annotate_1.30.0       digest_0.4.2
> [4] preprocessCore_1.14.0 splines_2.13.0
> [7] survival_2.36-8       tools_2.13.0          xtable_1.5-6
> 
> this is my raw data
> 
> AffyBatch object
> size of arrays=1050x1050 features (21 kb)
> cdf=exon.pmcdf (1411189 affyids)
> number of samples=12
> number of genes=1411189
> annotation=hugene10stv1
> notes=
> 
> 
> 
> 
> Thanks in advance
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