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Question: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
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6.1 years ago by
Andreas Heider290 wrote:
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&amp;categoryId=35765&amp;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]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > > [[alternative HTML version deleted]]