[BioC] Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays

[cstrato]

Dear Andreas,

As Jim already mentioned, package xps is able to preprocess MoExon 1.0 
ST arrays at the probeset and the gene level, see also my earlier reply 
to a similar question:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2012-June/045958.html

Best regards
Christian
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V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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On 6/13/12 4:47 PM, James W. MacDonald wrote:
> Hi Andreas,
>
> On 6/13/2012 3:14 AM, Andreas Heider wrote:
>> Dear mailing list,
>> I know this was on the list couple of times, and I think I read it
>> all, but
>> actually I still don't get it right. So here is my problem:
>>
>> I want to be able to work with Mouse Exon 1.0 ST Arrays (NOT Mouse
>> Gene 1.0
>> ST) in a similar fashion to eg. HG-U133 arrays.
>> That means, I want to finally have it accessible as an ExpressionSet
>> object
>> with a right Bioconductor annotation assigned. This should include GENE
>> SYMBOLS, RefSeq IDs and ENTREZ IDs.
>
> The problem here is that you want to do something that AFAIK isn't easy
> to do. The Gene ST arrays allow you to summarize all the probes that
> interrogate a particular transcript (e.g., all the exon-level probesets
> are collapsed to transcript level, and then you summarize). However, for
> the Exon ST arrays that isn't the case, unless there is something in xps
> to allow for that - I know next to nothing about that package, so
> Cristian Stratowa will have to chime in if I am missing something.
>
> For the Exon chips, you are always summarizing at the same probeset
> level, where there are <= 4 probes per probeset, and there can be any
> number of probesets that interrogate a given exon. Lots of these
> probesets interrogate regions that aren't even transcribed, according to
> current knowledge of the genome. When you choose core, extended or full
> probesets, you are just changing the number of probesets being used, not
> summarizing at a different level as with the Gene ST chip.
>
> So when you say you want gene symbols, refseq ids and gene ids, what
> exactly are you after? If a given probeset is in the intron of a gene do
> you want to annotate it as being part of that gene? How about if it is
> in the UTR (or really close to the UTR)? What do you want to do with the
> probesets where one or more of the probes binds in multiple positions in
> the genome? These are all questions that the exonmap package tries to
> consider, and it gets really complicated. That's why Affy went with the
> Gene ST chips - they unleashed the Exon chips on us and couldn't sell
> them because people were saying WTF do I do with this thing?
>
> I don't think there is an easy or obvious answer to your question. If
> you were to come up with what you think are reasonable answers to my
> questions, then it wouldn't be much work to extract the chr, start, end
> from the pd.moex.1.0.st.v1 package, and then use GenomicFeatures (e.g.,
> findOverlaps()) to decide what regions are being interrogated, and
> annotate from there.
>
> Best,
>
> Jim
>
>
>>
>> I can import it as a AffyBatch and generate an ExpressionSet with the
>> help
>> of the Xmap/exonmap supplied CDF, but there is no annotation attached
>> to it.
>>
>> OR
>>
>> I can import the CEL files with the "oligo" package as a Exon Array
>> object
>> and generate an ExpressionSet from it.
>> However in that case it still have no annotation.
>>
>> Surprisingly on the Bioconductor website there are all packages needed to
>> deal with Mouse Gene 1.0 ST arrays but the informtion to work with Mouse
>> Exon 1.0 ST arrays seems missing!
>>
>> What am I doing wrong here? Has someone else had such problems?
>>
>> Thanks in advance for your effort,
>> Andreas
>>
>> [[alternative HTML version deleted]]
>>
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>