The combined annotation function in gene.to.exon.probeset seems to return different results to combining gene.to.exon and exon.to.gene This example demonstrates: Can anyone help me understand what is happening here: > g<-"ENSG00000185201" > all.hits<-gene.to.exon.probeset(g,unique=TRUE,probes.min=4) > all.hits gene exon probeset_id probeset_name num_probes 2 ENSG00000185201 ENSE00001297940 807080 3315673 4 4 ENSG00000185201 ENSE00001540284 807080 3315673 4 #### now just the first step: > gene.to.exon(g,as.vector=TRUE,unique=TRUE,subset=c("core","est")) [1] "ENSE00001540295" "ENSE00001623765" "ENSE00001772457" "ENSE00001627970" [5] "ENSE00001623180" "ENSE00001540284" "ENSE00001792814" "ENSE00001297940" [9] "ENSE00001657933" "ENSE00001770875" So the combined function returns fewer exons that just gene.to.exon one of these "ENSE00001792814" has a valid probset: > e<-"ENSE00001792814" > exon.to.probeset(e,as.vector=FALSE,unique=FALSE,subset=c("core"),probe s.min=4) exon probeset_id probeset_name num_probes 1 ENSE00001792814 807077 3315670 4 > Only thing I can come up with is that gene.to.exon.probeset filters for multi-target probes since > is.exonic("3315670") 3315670 FALSE > is.multitarget("3315670",mt.level=1) [1] TRUE > But I can find no mention of this in the documentation can anyone confirm if this is the case ?? Thanks Paul > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.2.1 exon.pmcdf_1.1 exonmap_2.4.0 [4] RMySQL_0.7-4 RColorBrewer_1.0-2 genefilter_1.28.2 [7] affyPLM_1.22.0 preprocessCore_1.8.0 gcrma_2.18.1 [10] affycoretools_1.18.0 KEGG.db_2.3.5 GO.db_2.3.5 [13] RSQLite_0.8-1 DBI_0.2-5 AnnotationDbi_1.8.1 [16] affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 annaffy_1.18.0 annotate_1.24.1 biomaRt_2.2.0 [5] Biostrings_2.14.10 Category_2.12.0 GOstats_2.12.0 graph_1.24.2 [9] GSEABase_1.8.0 IRanges_1.4.9 RBGL_1.22.0 RCurl_1.3-1 [13] splines_2.10.1 survival_2.35-8 tcltk_2.10.1 tools_2.10.1 [17] XML_2.6-0 xtable_1.5-6 > -- Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo@uq.edu.au Web: http://www.di.uq.edu.au [[alternative HTML version deleted]]