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

Wed Jun 27 17:27:56 CEST 2012

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]]
>> >>>
>> >>> _______________________________________________
>> >>> Bioconductor mailing list
>> >>> Bioconductor at r-project.org
>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >>> Search the archives:
>> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>
>> >>
>> >> --
>> >> James W. MacDonald, M.S.
>> >> Biostatistician
>> >> University of Washington
>> >> Environmental and Occupational Health Sciences
>> >> 4225 Roosevelt Way NE, # 100
>> >> Seattle WA 98105-6099
>> >>
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor