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

[Tim Yates]

Sorry, my phone decided to send this response off list...

---

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


On 28/04/2011 08:54, "Gomez Moruno, Antonio" <agomezm at idibell.cat> wrote:

> 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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