Hi Julie,
I just had a quick look at that probeset on X:Map - here:
(http://xmap.picr.man.ac.uk). There's quite a bit of info here, including
the hit location of each individual probe in the probeset - what comes back
is that those probesets land in an intron.

There's help pages on the website, but if you search for the probeset (you
might need to set the species first), it will appear in the 'Selection
Details' window in the middle below the browser. Clicking on the '[+]' by
the probeset name expands the annotation tree to reveal each probe and then
if you expand the tree under each probe, the places where they match to the
genome. To the right of this window, you'll see some green arrows. If you
click on these, it'll make the browser jump to the appropriate position...
Sorry that's a lot easier to do than to write, I think!

...anyway, it seems that the probesets are annotated as 'intronic'. This
means that one or more of the probes don't hit an exon, as defined by
ENSEMBL... 

In R, the function call:

> is.intronic(c('4448480','4305509'))
4448480 4305509 
   TRUE    TRUE 


confirms this. (If this is the first time you've run this command, it might
take a few seconds while it builds a local cache to (ultimately) speed
things up. The second time you call it, it should be a lot quicker.)

Crispin





On 13/12/2010 17:45, "Zhu, Lihua (Julie)" <Julie.Zhu@umassmed.edu> wrote:

> Hi Tim,
> 
> Thanks so much for such a quick response!
> 
> Here is a probeset ID that maps to a gene but not to any exon or transcript.
> 
> 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=TRUE)
> #[1] "ENSMUSG00000021708"
> 
> I looked up the detailed information of this probeset as follows.
> probeset.details("4448480")
> stable_id array_name probe_count hit_score gene_score transcript_score
> 1   4448480   MoEx-1_0           4         1          1                0
>   exon_score est_gene_score est_transcript_score est_exon_score
> 1          0              0                    0              0
>   prediction_transcript_score prediction_exon_score protein_score
> 1                           0                     0             0
>   domain_score
> 1            0
> 
> It looks like this probeset has one or more of its probes missing the
> transcript/exon target but uniquely aligned to a gene. Is it correct that this
> probeset is mapped to the un-transcribed region of the gene?
> 
> Here is an example that a probeset is mapped to both gene and transcript but
> not to any exon.
> 
> probeset.details("4305509")
>   stable_id array_name probe_count hit_score gene_score transcript_score
> 1   4305509   MoEx-1_0           4         1          1                2
>   exon_score est_gene_score est_transcript_score est_exon_score
> 1          0              1                    2              0
>   prediction_transcript_score prediction_exon_score protein_score
> 1                           1                     0             0
>   domain_score
> 1            0
> 
> Is it correct that this probeset is aligned to the intron region of the
> transcript?
> 
> Thanks so much for your help!
> 
> Best regards,
> 
> Julie
> 
> 
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