[BioC] mogene10stprobeset.db error

[Vincent Carey]

Please keep responses on list.  I am glad your results seem to make
more sense now.  nevertheless, a tightening of the
preprocessing/analysis/annotation pipeline for affy gene/exon 1.0 st
arrays would be welcome, and the oligo package addresses this to some
extent.  more fully worked examples for these arrays are in
development.

On Sun, Jul 4, 2010 at 5:19 AM, Maxim <deeepersound at googlemail.com> wrote:
> Ooops, sorry, I was not aware of the complexity of the situation.
> Meanwhile I found out that using the (before not specified)
> mogene-1_0-st-v1,r3.cdf I anyhow just get the gene summaries and not
> the individual probesets for individual exons (ending up in roughly
> 35000 IDs as compared to the larger 10^6 total IDs/probes), at least
> when using the "short" protocol as suggested on the aroma homepage. I
> use latest aroma and R 2.10!
>
> According to this situation I found an older mailing list that
> suggested to use the mogene10sttranscriptcluster.db instead. Ineed,
> this solved all my problems (most of it, still a number if IDs are not
> idnetified).
>
> Anyhow, for my toptable presentation in Limma it's fine.
>
> Thanks you!
>
> Maxim
>
> 2010/7/4 Vincent Carey <stvjc at channing.harvard.edu>:
>> Others will have to comment on the details of this mapping.  You are
>> finding a "hit" to an eight-digit token of weakly specified provenance
>> (generated with aroma, no indication of version etc) and asserting
>> that an "ID is clearly correct", without telling us the resource where
>> you found the "hit".  We can use biomart to follow up a bit
>>
>>> library(biomaRt)
>>> ss = useDataset("mmusculus_gene_ensembl", mart=useMart("ensembl"))
>>> fff = getBM(mart=ss, filters="affy_mogene_1_0_st_v1", values="10471503", attributes=c("ensembl_gene_id",
>> +  "ensembl_transcript_id", "chromosome_name", "mgi_symbol"))
>>> fff
>>     ensembl_gene_id ensembl_transcript_id chromosome_name mgi_symbol
>> 1 ENSMUSG00000088569    ENSMUST00000157944               2         NA
>> 2 ENSMUSG00000065226    ENSMUST00000083292               9         NA
>> 3 ENSMUSG00000088929    ENSMUST00000158304               9         NA
>> 4 ENSMUSG00000065282    ENSMUST00000083348               9         NA
>>
>> suggesting that current ensembl annotation maps "the ID" to
>> transcripts on chr 2 and chr 9.  Perhaps biomaRt will yield more clues
>> for you.
>>
>>> sessionInfo()
>> R version 2.12.0 Under development (unstable) (2010-06-30 r52417)
>> Platform: x86_64-apple-darwin10.3.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>>  [1] grid      splines   stats     graphics  grDevices datasets  tools
>>  [8] utils     methods   base
>>
>> other attached packages:
>>  [1] biomaRt_2.5.1                        mogene10stprobeset.db_5.0.2
>>  [3] mogene10sttranscriptcluster.db_5.0.1 org.Mm.eg.db_2.4.1              etc...
>>
>>
>> On Sat, Jul 3, 2010 at 4:02 PM, Maxim <deeepersound at googlemail.com> wrote:
>>> Hi,
>>>
>>> I try to analyze MoGene-1_0-st gene arrays. I used the aroma package
>>> to do this and came up with an expression matrix, but have no clue,
>>> how to assign real gene names to the respective "IDs" (column "item
>>> numbers" after aroma normalization and summarization).
>>>
>>> As a workaround I simply tried to load the mogene10stprobeset.db library and did
>>>
>>> u<-mget(row.names(x),mogene10stprobesetSYMBOL)
>>>
>>> with x being the expression matrix and rownames(x) are the IDs. But
>>> the majority of IDs are unknown:
>>>
>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>>>  value for "10471503" not found
>>>
>>> But why? This ID is clearly correct:
>>> 10471503                chr2:32530629-32530765  chr2    NC_000068.6     +       32530629        32530765        25      ---     ENSMUST00000082819
>>> // ENSEMBL // ncrna:snoRNA chromosome:NCBIM37:2:32530629:32530765:1
>>> gene:ENSMUSG00000064753 // chr2 // 100 // 100 // 25 // 25 // 0 ///
>>> ENSMUST00000083292 // ENSEMBL // ncrna:snoRNA
>>> chromosome:NCBIM37:9:15119289:15119425:1 gene:ENSMUSG00000065226 //
>>> chr2 // 72 // 100 // 18 // 25 // 0      main
>>>
>>> What is my problem, obviously I miss something?
>>>
>>> Maxim
>>>
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>>>
>>
>