I am trying to build an annotation package for Affy's Moe430 2.0 array (since it does not appear to be available under the metadata section) and I am wondering if my approach is the same as is used to build the "official" metadata packages. What I did was to simply use the annotation available from Affymetrix to map each probe id to its corresponding genbank id using the file: http://www.affymetrix.com/Auth/analysis/downloads/taf/Mouse430_2_annot _csv.zip and then run ABPkgBuilder as detailed in the vignette "How to use AnnBuilder." The reason for my concern is that the QC stats my efforts returned indicate that I have fewer probes annotated then the sum of the QC stats for the moe430a and moe430b packages would give me. Here's what my moe430_2QC.rda contains: Quality control information for moe430_2 Date built: Wed Oct 20 13:46:14 2004 Number of probes: 45102 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: moe430_2ACCNUM found 45102 of 45102 moe430_2CHR found 31093 of 45102 moe430_2CHRLOC found 21050 of 45102 moe430_2ENZYME found 1469 of 45102 moe430_2GENENAME found 31297 of 45102 moe430_2GO found 17752 of 45102 moe430_2GRIF found 0 of 45102 moe430_2LOCUSID found 31362 of 45102 moe430_2MAP found 28106 of 45102 moe430_2OMIM found 0 of 45102 moe430_2PATH found 2757 of 45102 moe430_2PMID found 29071 of 45102 moe430_2REFSEQ found 25512 of 45102 moe430_2SUMFUNC found 0 of 45102 moe430_2SYMBOL found 31298 of 45102 moe430_2UNIGENE found 30800 of 45102 Mappings found for non-probe based rda files: moe430_2CHRLENGTHS found 21 moe430_2ENZYME2PROBE found 387 moe430_2GO2ALLPROBES found 4483 moe430_2GO2PROBE found 3252 moe430_2ORGANISM found 1 moe430_2PATH2PROBE found 122 moe430_2PMID2PROBE found 21108 However, for example, the sum of moe430aGO (found 15262 of 22690) and moe430bGO (found 4499 of 22575) listed under the metadata section indicates that merging these two packages --after all, the moe430 2.0 array is just that, a merge of the A and B chips-- would give me more annotations than my efforts produced, which is unexpected given that the moe430a and moe430b packages were created > 6 months ago. Has something changed within the AnnBuilder package (I'm using version 1.4.18 under linux) or the sources used for annotation (I used getSrcUrl("all", organism="Mus Musculus") to src the various annotation files) that would explain these results? Best, Jeff __________________________________ Jeffrey Rasmussen Research Consultant, Bioinformatics Department of Immunology University of Washington

If you are using R-2.0.0, there is a devel version of moe4302 that you can get using reposTools. library(reposTools) install.packages2("moe4302", develOK=TRUE) You might compare this with what you got. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> jeffrey rasmussen <rasmuss@u.washington.edu> 10/20/04 5:58 PM >>> I am trying to build an annotation package for Affy's Moe430 2.0 array (since it does not appear to be available under the metadata section) and I am wondering if my approach is the same as is used to build the "official" metadata packages. What I did was to simply use the annotation available from Affymetrix to map each probe id to its corresponding genbank id using the file: http://www.affymetrix.com/Auth/analysis/downloads/taf/Mouse430_2_annot _csv.zip and then run ABPkgBuilder as detailed in the vignette "How to use AnnBuilder." The reason for my concern is that the QC stats my efforts returned indicate that I have fewer probes annotated then the sum of the QC stats for the moe430a and moe430b packages would give me. Here's what my moe430_2QC.rda contains: Quality control information for moe430_2 Date built: Wed Oct 20 13:46:14 2004 Number of probes: 45102 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: moe430_2ACCNUM found 45102 of 45102 moe430_2CHR found 31093 of 45102 moe430_2CHRLOC found 21050 of 45102 moe430_2ENZYME found 1469 of 45102 moe430_2GENENAME found 31297 of 45102 moe430_2GO found 17752 of 45102 moe430_2GRIF found 0 of 45102 moe430_2LOCUSID found 31362 of 45102 moe430_2MAP found 28106 of 45102 moe430_2OMIM found 0 of 45102 moe430_2PATH found 2757 of 45102 moe430_2PMID found 29071 of 45102 moe430_2REFSEQ found 25512 of 45102 moe430_2SUMFUNC found 0 of 45102 moe430_2SYMBOL found 31298 of 45102 moe430_2UNIGENE found 30800 of 45102 Mappings found for non-probe based rda files: moe430_2CHRLENGTHS found 21 moe430_2ENZYME2PROBE found 387 moe430_2GO2ALLPROBES found 4483 moe430_2GO2PROBE found 3252 moe430_2ORGANISM found 1 moe430_2PATH2PROBE found 122 moe430_2PMID2PROBE found 21108 However, for example, the sum of moe430aGO (found 15262 of 22690) and moe430bGO (found 4499 of 22575) listed under the metadata section indicates that merging these two packages --after all, the moe430 2.0 array is just that, a merge of the A and B chips-- would give me more annotations than my efforts produced, which is unexpected given that the moe430a and moe430b packages were created > 6 months ago. Has something changed within the AnnBuilder package (I'm using version 1.4.18 under linux) or the sources used for annotation (I used getSrcUrl("all", organism="Mus Musculus") to src the various annotation files) that would explain these results? Best, Jeff __________________________________ Jeffrey Rasmussen Research Consultant, Bioinformatics Department of Immunology University of Washington _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

>Thanks for the suggestion, that seemed to do the trick. Note that the >package is apparently called "moe430v2," which seems to be inconsistent >with how the probe and cdf packages are named ("mouse4302"). We actually have mouse4302 in the devel track. moe430v2 will go soon. > >Jeff. >__________________________________ >Jeffrey Rasmussen >Research Consultant, Bioinformatics >Department of Immunology >University of Washington >__________________________________ > >On Wed, 20 Oct 2004, James MacDonald wrote: > >> If you are using R-2.0.0, there is a devel version of moe4302 that you >> can get using reposTools. >> >> library(reposTools) >> install.packages2("moe4302", develOK=TRUE) >> >> You might compare this with what you got. >> >> HTH, >> >> Jim >> >> >> >> James W. MacDonald >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >>>>> jeffrey rasmussen <rasmuss@u.washington.edu> 10/20/04 5:58 PM >>> >> I am trying to build an annotation package for Affy's Moe430 2.0 array >> (since it does not appear to be available under the metadata section) >> and >> I am wondering if my approach is the same as is used to build the >> "official" metadata packages. >> >> What I did was to simply use the annotation available from Affymetrix to >> >> map each probe id to its corresponding genbank id using the file: >> http://www.affymetrix.com/Auth/analysis/downloads/taf/Mouse430_2_annot _csv.zip >> and then run ABPkgBuilder as detailed in the vignette "How to use >> AnnBuilder." >> >> The reason for my concern is that the QC stats my efforts returned >> indicate that I have fewer probes annotated then the sum of the QC stats >> >> for the moe430a and moe430b packages would give me. >> >> Here's what my moe430_2QC.rda contains: >> >> Quality control information for moe430_2 >> Date built: Wed Oct 20 13:46:14 2004 >> Number of probes: 45102 >> Probe number missmatch: None >> Probe missmatch: None >> Mappings found for probe based rda files: >> moe430_2ACCNUM found 45102 of 45102 >> moe430_2CHR found 31093 of 45102 >> moe430_2CHRLOC found 21050 of 45102 >> moe430_2ENZYME found 1469 of 45102 >> moe430_2GENENAME found 31297 of 45102 >> moe430_2GO found 17752 of 45102 >> moe430_2GRIF found 0 of 45102 >> moe430_2LOCUSID found 31362 of 45102 >> moe430_2MAP found 28106 of 45102 >> moe430_2OMIM found 0 of 45102 >> moe430_2PATH found 2757 of 45102 >> moe430_2PMID found 29071 of 45102 >> moe430_2REFSEQ found 25512 of 45102 >> moe430_2SUMFUNC found 0 of 45102 >> moe430_2SYMBOL found 31298 of 45102 >> moe430_2UNIGENE found 30800 of 45102 >> Mappings found for non-probe based rda files: >> moe430_2CHRLENGTHS found 21 >> moe430_2ENZYME2PROBE found 387 >> moe430_2GO2ALLPROBES found 4483 >> moe430_2GO2PROBE found 3252 >> moe430_2ORGANISM found 1 >> moe430_2PATH2PROBE found 122 >> moe430_2PMID2PROBE found 21108 >> >> However, for example, the sum of moe430aGO (found 15262 of 22690) and >> moe430bGO (found 4499 of 22575) listed under the metadata section >> indicates that merging these two packages --after all, the moe430 2.0 >> array is just that, a merge of the A and B chips-- would give me more >> annotations than my efforts produced, which is unexpected given that the >> >> moe430a and moe430b packages were created > 6 months ago. Has something >> changed within the AnnBuilder package (I'm using version 1.4.18 under >> linux) or the sources used for annotation (I used getSrcUrl("all", >> organism="Mus Musculus") to src the various annotation files) that would >> >> explain these results? >> >> Best, >> Jeff >> __________________________________ >> Jeffrey Rasmussen >> Research Consultant, Bioinformatics >> Department of Immunology >> University of Washington >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084