Dear List, I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am interested in differential expression at probeset and at gene level. Searching the list archives reveals, that "makecdfenv and makePlatformDesign make the assumption that there is a one-to-one mapping of probe ==> probeset", which is not true for the Human Gene 1.0 chip. Anyway, I found some interesting packages: - exonmap: Looks promising, but there are no cdf files for the Gene 1.0 Chip on the related website (just for the Exon 1.0) - xps: This seems to be a completely new infrastructure for affymetrix chips, which is capable of reading the Gene 1.0 Chip. - aroma.affymetrix: This is not a BioC package. (Why not?) Have I overseen a package? Can someone point me to further information regarding BioC and the Human Gene Chip? I am not sure where to start and appreciate any comments and experiences of other users. Best wishes, Hans-Ulrich PS: Is there any work going on the integration the Human / Exon Chip in the affy packages? Or are these Chips too different from the conventional 3' Chips.

Dear Hans-Ulrich Although I think that there is a cdfenv for the HuGene array, which can be used with 'affy', it may always be a good idea to try different packages. I believe that for the HuGene array my package 'xps' may have some advantages: - it parses the original Affymetrix CLF, PGF and annotation files - in addition to RMA normalization you can also do DABG and even MAS5 detection calls - it works on computers with 1GB RAM only In any case I would be very interested in user's feedback, and would appreciate if you would give it a try. Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Hans-Ulrich Klein wrote: > Dear List, > > I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am > interested in differential expression at probeset and at gene level. > Searching the list archives reveals, that "makecdfenv and > makePlatformDesign make the assumption that there is a one-to-one > mapping of probe ==> probeset", which is not true for the Human Gene > 1.0 chip. > > Anyway, I found some interesting packages: > - exonmap: Looks promising, but there are no cdf files for the Gene > 1.0 Chip on the related website (just for the Exon 1.0) > - xps: This seems to be a completely new infrastructure for affymetrix > chips, which is capable of reading the Gene 1.0 Chip. > - aroma.affymetrix: This is not a BioC package. (Why not?) > > Have I overseen a package? Can someone point me to further information > regarding BioC and the Human Gene Chip? I am not sure where to start > and appreciate any comments and experiences of other users. > > Best wishes, > Hans-Ulrich > > PS: Is there any work going on the integration the Human / Exon Chip > in the affy packages? Or are these Chips too different from the > conventional 3' Chips. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >

Hi, RE exonmap... The package offers annotation mapping from probeset locations (we annotated the arrays against the whole genome) to the genes, transcripts and exons at that position, along with mappings between the different levels of annotation). I'm not sure how useful it would be in the context of Gene level arrays - but given a gene symbol or genomic location, it should be straightforward to map to the corresponding transcripts and exons. The easiest way to see what information is represented in the package is to have a look at the accompanying genome browser at: http://map.picr.man.ac.uk Crispin On 7/5/08 19:44, "Hans-Ulrich Klein" <h.klein at="" uni-muenster.de=""> wrote: > Dear List, > > I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am > interested in differential expression at probeset and at gene level. > Searching the list archives reveals, that "makecdfenv and > makePlatformDesign make the assumption that there is a one-to-one > mapping of probe ==> probeset", which is not true for the Human Gene 1.0 > chip. > > Anyway, I found some interesting packages: > - exonmap: Looks promising, but there are no cdf files for the Gene 1.0 > Chip on the related website (just for the Exon 1.0) > - xps: This seems to be a completely new infrastructure for affymetrix > chips, which is capable of reading the Gene 1.0 Chip. > - aroma.affymetrix: This is not a BioC package. (Why not?) > > Have I overseen a package? Can someone point me to further information > regarding BioC and the Human Gene Chip? I am not sure where to start and > appreciate any comments and experiences of other users. > > Best wishes, > Hans-Ulrich > > PS: Is there any work going on the integration the Human / Exon Chip in > the affy packages? Or are these Chips too different from the > conventional 3' Chips. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}

Dear Benilton, thanks for your reponse. I built a pdInfoPackage as suggested: library(pdInfoBuilder) pgfFile = "HuGene-1_0-st-v1.r3.pgf" clfFile = "HuGene-1_0-st-v1.r3.clf" probeFile = "HuGene-1_0-st-v1.probe.tab" transFile = "HuGene-1_0-st-v1.na24.hg18.transcript.csv" pkg <- new("AffyGenePDInfoPkgSeed", version="0.0.1", author="Hans-Ulrich Klein", email="h.klein at uni- muenster.de", biocViews="AnnotationData", genomebuild="hg18", pgfFile=pgfFile, clfFile=clfFile, probeFile=probeFile, transFile=transFile) makePdInfoPackage(pkg, destDir=".") Creating package in ./pd.hugene.1.0.st.v1 loadUnitsByBatch took 67.19 sec loadAffyCsv took 9.10 sec loadAffySeqCsv took 95.06 sec DB sort, index creation took 32.30 sec Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I installed the package and built an ExpressionSet using RMA normalized probeset values exported from Affymetrix "Expression Console". Currently I am using the package by sending SQL statements directly, e.g.: > library("pd.hugene.1.0.st.v1") > con = db(pd.hugene.1.0.st.v1) > dbListTables(con) [1] "featureSet" "mmfeature" "pm_mm" "pmfeature" "qcmmfeature" [6] "qcpm_qcmm" "qcpmfeature" "sequence" "sqlite_stat1" "table_info" > featureNames(eSet)[10000] [1] "7973403" > res = dbSendQuery(con, "SELECT * FROM FeatureSet WHERE fsetid == 7973403;") > table = fetch(res) > table$gene_assignment [1] "NM_138460 // CMTM5 // CKLF-like MARVEL transmembrane domain containing 5 // 14q11.2 // 116173 /// NM_001037288 // CMTM5 // CKLF- like MARVEL transmembrane domain containing 5 // 14q11.2 // 116173 /// ENST00000359320 // CMTM5 // CKLF-like MARVEL transmembrane domain containing 5 (CMTM5), transcript variant 1, mRNA // 14q11.2 // 116173 /// ENST00000382809 // CMTM5 // CKLF-like MARVEL transmembrane domain containing 5 (CMTM5), transcript variant 3, mRNA // 14q11.2 // 116173 /// AF527413 // CMTM5 // CKLF-like MARVEL transmembrane domain containing 5 // 14q11.2 // 116173 /// AK094840 // CMTM5 // CKLF-like MARVEL transmembrane domain containing 5 // 14q11.2 // 116173" This is OK for me at the moment, but it is laborious compared to classic annotation data packages (like "hgu95av2.db"). Is there a more convenient way to access annotation data? Thanks in advance, Hans-Ulrich