[BioC] Xmapcore package

[Zhu, Lihua (Julie)]

Tim,

While annotating a list of probesets to exons, transcripts and genes, I
noticed that there are more probesets (e.g.,4448480) mapped to genes than
those mapped to transcripts and the least number of probesets mapped to the
exons. Is this expected? I suppose if one probe is aligned to multiple exons
in a gene, then the exon mapping was removed while the gene mapping was
kept. Could you please elaborate? Thanks so much for your help!

Best regards,

Julie

library(xmapcore)
xmap.connect("mouse")
>probeset.to.transcript("4448480", as.vector=FALSE)
NULL
> probeset.to.exon("4448480", as.vector=FALSE)
NULL
> probeset.to.gene("4448480", as.vector=FALSE)
RangedData with 1 row and 9 value columns across 1 space
        space               ranges |         IN1          stable_id
strand
  <character>            <IRanges> | <character>        <character>
<integer>
1          13 [92020005, 92901611] |     4448480 ENSMUSG00000021708
-1
         biotype      status
     <character> <character>
1 protein_coding       KNOWN
                   
description
                   
<character>
1 RAS protein-specific guanine nucleotide-releasing factor 2 Gene
[Source:MGI (curated);Acc:MGI:109137]
  db_display_name      symbol
      <character> <character>
1   MGI (curated)     Rasgrf2
                                               symbol_description
                                                      <character>
1 RAS protein-specific guanine nucleotide-releasing factor 2 Gene
> temp= transcript.to.probeset(gene.to.transcript(probeset.to.gene("4448480",
as.vector=TRUE), as.vector=TRUE), as.vector=FALSE)

> temp[temp$stable_id == "4448480",]
 [1] IN1                         stable_id
 [3] array_name                  probe_count
 [5] hit_score                   gene_score
 [7] transcript_score            exon_score
 [9] est_gene_score              est_transcript_score
[11] est_exon_score              prediction_transcript_score
[13] prediction_exon_score       protein_score
[15] domain_score  
<0 rows> (or 0-length row.names)

 sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] mouseexonpmcdf_1.1 xmapcore_1.2.8     digest_0.4.2
[4] IRanges_1.6.11     RMySQL_0.7-5       DBI_0.2-5

loaded via a namespace (and not attached):
[1] tools_2.11.1