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

Wed Jun 27 17:44:07 CEST 2012

That's correct... the summarisation step does use the MPS... and I'll
add support for our next release. b

On 27 June 2012 16:37, James Perkins <jperkins at biochem.ucl.ac.uk> wrote:
> 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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