Thanks for the quick answer!
Sadly I've already been at that point. The problem here is, that I then
have a table with a column "gene_assignment" that has EVERY single
identifier in it just separated by "//" or "///".
I can not reliably extract the information I want from it, because
sometimes there is no RefSeq or whatsoever and the second (or third) item
after the next "//" is used.

No I mean there has to be a way to get an ExpressionSet object from the
MoEx 1.0 ST array with IDs in a way I can map them to a annotation such as
"mouse4302SYMBOL" or "mouse4302ENTREZID" as it would work on ANY other
array type (including Mouse Gene 1.0 ST arrays).

How am I gonna' get there?

2012/6/13 Morgane Boone <Morgane.Boone@ugent.be>

> You can find the annotations on the affymetrix website, right here:
> http://www.affymetrix.com/**estore/browse/products.jsp?**
> productId=131474&categoryId=**35765&productName=GeneChip-**
> Mouse-Exon-1.0-ST-Array#1_3<http://www.affymetrix.com/estore/browse/products.jsp?productId=131474&categoryId=35765&productName=GeneChip-Mouse-Exon-1.0-ST-Array#1_3>
> under the section `NetAffx annotation files`. You can simply load it in R
> and merge it to whatever table you have with the probeset IDs. Something
> like what I use for the Human Exon arrays (this example is for the
> transcript level analysis, it is the same when working on exon level, then
> you just use the probeset annotation csv file):
>
> hekannotfile <- "HuEx-1_0-st-v2.na29.hg18.**transcript.csv"
> hekanTable <- read.table(hekannotfile, sep=",", header=TRUE,
> quote="\"",row.names=1)
> colnames(hekanTable)
> # [1] "probeset_id"           "seqname"               "strand"
>  [4] "start"                 "stop"                  "total_probes"
>  [7] "gene_assignment"       "mrna_assignment"       "swissprot"
> [10] "unigene"               "GO_biological_process"
> "GO_cellular_component"
> [13] "GO_molecular_function" "pathway"               "protein_domains"
> [16] "category"
>
> # where b is my list of filtered genes
> a <- hekanTable[rownames(b),]
> annotatedlist <-merge(b,a, by.x="probeset_id")
>
> Hope this helps.
>
> Morgane
>
>
>
> Quoting "Andreas Heider" <aheider@trm.uni-leipzig.de>:
>
>  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.
>>
>> 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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>>
>>
>
>
>

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