problems with Affymetrix probes id using exonmap and xmapcore
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@gomez-moruno-antonio-4604
Last seen 8.4 years ago
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
Annotation cdf exonmap xmapcore Annotation cdf exonmap xmapcore • 614 views
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