

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"),probes.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




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