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

Wed Jun 27 17:37:54 CEST 2012

Sorry, I meant at the rma(target=) level, not the getNetAffx level,
which I *assume* uses the mps files to map between ps and transcripts?

Cheers,

Jim

On 27 June 2012 17:27, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
> Hi Jim,
>
> I'll make sure to add the comprehensive MPS as soon as I get more info
> about it from the specialists...
>
> However, note that the contents of the MPS files are not used by
> getNetAffx(), which only uses the probeset/transcript annotation
> file...
>
> Thanks,
>
> benilton
>
> On 27 June 2012 15:00, James Perkins <jperkins at biochem.ucl.ac.uk> wrote:
>> Hi,
>>
>> I wasn't sure if this was worth starting a new thread for this, since
>> my question is very much related to this thread...
>>
>> Is there any plan to include the "comprehensive" exon array mappings?
>>
>> E.g. for rat:
>>
>> If one goes here
>>
>> http://www.affymetrix.com/estore/browse/products.jsp?productId=131489&categoryId=35748&productName=GeneChip-Rat-Exon-1.0-ST-Array#1_1
>>
>> Then to Technical Documentation tab
>>
>> And downloads the
>>
>> "Rat Exon 1.0 ST Array Probeset, and Meta Probeset Files, core, full,
>> extended and comprehensive rn4" data
>>
>> http://www.affymetrix.com/Auth/support/downloads/library_files/RaEx-1_0-st-v1.r2.dt1.rn4.ps.zip
>>
>> There are the core/extended/full ps and mps files here.
>>
>> However there is also a comprehensive mps file.
>>
>> Full, core and extended are from 2006.
>>
>> The comprehensive is from 2010 (and gets updated more regularly), so
>> perhaps would be a better file to use for getNetAffx ?
>>
>> Apologies if this has been covered before. I am never sure of what is
>> the best way to analyse exon array data at the gene level.
>>
>> Thanks,
>>
>> Jim
>>
>>
>>
>>
>> On 13 June 2012 21:37, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
>>>
>>> please correct the code below to:
>>>
>>> eset = rma(raw, target='full') ## or 'core', 'extended' (whatever is available)
>>>
>>> and if you want results at the exon level
>>>
>>> eset = rma(raw, target='probeset')
>>> featureData(eset) = getNetAffx(raw, 'probeset')
>>>
>>> apologies for the mistake below.
>>>
>>> b
>>>
>>> On 13 June 2012 20:11, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
>>> > FWIW, remember that you can obtain the contents of the annotation
>>> > files (the NA32 Affymetrix files) with:
>>> >
>>> > library(Biobase)
>>> > library(oligo)
>>> > raw = read.celfiles(list.celfiles())
>>> > eset = rma(raw, target='transcript')
>>> > featureData(eset) = getNetAffx(eset, 'transcript')
>>> > head(fData(eset))
>>> >
>>> > b
>>> >
>>> > On 13 June 2012 15:47, James W. MacDonald <jmacdon at uw.edu> 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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>>> >>
>>> >>
>>> >> --
>>> >> James W. MacDonald, M.S.
>>> >> Biostatistician
>>> >> University of Washington
>>> >> Environmental and Occupational Health Sciences
>>> >> 4225 Roosevelt Way NE, # 100
>>> >> Seattle WA 98105-6099
>>> >>
>>> >>
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>>>
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