Question: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
gravatar for Andreas Heider
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 <> > You can find the annotations on the affymetrix website, right here: >**estore/browse/products.jsp?** > productId=131474&categoryId=**35765&productName=GeneChip-** > Mouse-Exon-1.0-ST-Array#1_3<http:"" 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" <>: > > 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 >> >>**listinfo/bioconductor<https: stat.e="""" mailman="" listinfo="" bioconductor=""> >> Search the archives:** >> science.biology.informatics.**conductor<http:"" gmane="" .science.biology.informatics.conductor=""> >> >> > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.1 years ago by Andreas Heider290
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 171 users visited in the last hour