Hi Kripa. Have a look at the Affymetrix website:
http://www.affymetrix.com/estore/browse/products.jsp?productId=131452&categoryId=35676&productName=GeneChip-Human-Exon-1.0-ST-Array#1_3 Click on "Technical Documentation" and the file you are probably after is "HuEx-1_0-st-v2 Transcript Cluster Annotations, CSV, Release 31 (25 MB 08/27/10)": http://www.affymetrix.com/Auth/analysis/downloads/na31/wtexon/HuEx-1_0-st-v2.na31.hg19.transcript.csv.zip The 'unitName' below is a transcript cluster id. You may have to parse the other columns to extract the gene identifiers/symbols. There are of course other ways to do this. For example, you may be able to use the 'exonmap' R/Bioconductor package. Hope that helps. Mark On 2011-01-24, at 3:29 PM, kripa raman wrote: > Hi, > I'm very new to microarray analysis and I fear I'm in too deep by starting > with the HuEx1_0-st-v2 chip, especially since no one in my building seems to > have conducted this analysis! > > Experiment currently: 2 chips have been analyzed and have had the same > treatment, I'm looking to confirm that the genes/ exons are the same for both > chips (ideally by identifying that the top 100 genes are identical) > > The issue I'm having is converting the unitName and groupName, currently seen > in the trFit table, into meaningful gene ID. I'm under the impression that I > should be connecting this with the csv file but I'm not sure how to go about > doing this. > Any help would be greatly appreciated! > > -Kripa > > > > Code thus far: > chipType<-"HuEx-1_0-st-v2" > > cdf<-AffymetrixCdfFile$ > byChipType(chipType, tags="coreR2,A20070914,EP") ##set cdf: Core probesets: > 18,708 units/transcript clusters, 284,258 groups/probesets, and 1,082,385 > probes > > cs<-AffymetrixCelSet$byName("control", cdf=cdf) ##set cel group: 0035 and 0028 > > > bc <- RmaBackgroundCorrection(cs, tag="coreR2") ##background correction > csBC <- process(bc,verbose=verbose) > > > qn <- QuantileNormalization(csBC, typesToUpdate="pm") ##normalization > csN <- process(qn, verbose=verbose) > MNorm<-extractMatrix(csN) > > > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) ##summarize > fit(plmTr, verbose=verbose) > > qamTr <- QualityAssessmentModel(plmTr) ##quality assessment > plotNuse(qamTr) > plotRle(qamTr) > > cesTr <- getChipEffectSet(plmTr) > trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE) > MSumm<-extractMatrix(cesTr) > > #####result (how do i go about changing this unitName and groupName) > unitName groupName unit group cell HuEx1_0028 HuEx1_0035 > 1 2315373 2315374 1 1 1 6.722633 4.735021 > 2 2315554 2315586 2 1 5 9.422164 9.943003 > 3 2315633 2315638 3 3 20 6.146615 6.00318 > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: mrobin...@wehi.edu.au e: m.robin...@garvan.org.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
