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

[Benilton Carvalho]

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