AnnBuilder to build annotation package for hs133phsentrezg
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@tineke-casneuf-2579
Last seen 8.2 years ago
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.3 years ago
United States
Tineke Casneuf wrote: > Dear list, > > I am trying to build an Annotation package for the hgu133plus2 array (Affy > array, human). For my data analysis I have been using the remapped > hs133phsentrezgcdf package. An annotation package exists for this CDF but > the contained information is very limited. So I decided to build my own, > using AnnBuilder. > Here's the code I used: > > ##### > library(AnnBuilder) > library(hs133phsentrezgcdf) > fN <- ls(hs133phsentrezgcdf) # to extract the featureNames in this CDF > cfN <- sub("_at", "", fN) # to obtain the entrez gene IDs > > ## construct the base file > mygeneNMap <- matrix(c(fN, cfN), byrow=F, ncol =2) > write.table(mygeneNMap, file = "geneNMap", sep = "\t", quote = FALSE, > row.names = FALSE, col.names = FALSE) > > ## retrieve where to go look for the info > mySrcUrls <- getSrcUrl("all", "Homo sapiens") > > myDir <- "." > > mySrcUrls <- getSrcUrl("all", "Homo sapiens") > > ABPkgBuilder(baseName = "geneNMap", srcUrls = mySrcUrls, > baseMapType = "ll", pkgName = "hs133phsentrezgannot", > pkgPath = ".", organism = "Homo sapiens", version = "1.1.0", > author = list(authors = "Tine Casneuf", maintainer = > "Tine, <tineke.casneuf at="" gmail.com"),="" fromweb="TRUE)"> ###### > > My baseName file has the probeset IDs in the first column, the Entrez Gene > ID in the second and thus looks like this: > > read.table(file = "geneNMap", sep ="\t")[1:4,] > V1 V2 > 1 1_at 1 > 2 10_at 10 > 3 100_at 100 > 4 1000_at 1000 > > The ABPkgBuilder function runs without errors or significant warnings. The > package build and can be installed but no mapping could be done for my data, > as you can see below: > > >> hs133phsentrezgannot() >> > > Quality control information for hs133phsentrezgannot > Date built: Created: Thu Jan 10 11:55:27 2008 > > Number of probes: 17589 > Probe number missmatch: None > Probe missmatch: None > Mappings found for probe based rda files: > hs133phsentrezgannotCHRLOC found 0 of 17589 > hs133phsentrezgannotENTREZID found 0 of 17589 > hs133phsentrezgannotENZYME found 0 of 17589 > hs133phsentrezgannotPATH found 0 of 17589 > Mappings found for non-probe based rda files: > hs133phsentrezgannotCHRLENGTHS found 25 > hs133phsentrezgannotORGANISM found 1 > hs133phsentrezgannotPFAM found 0 > hs133phsentrezgannotPROSITE found 0 > Does anyone have a clue what I am doing wrong? It will probably be something > small, but I cannot figure it out. > > Many thanks in advance! > Best, > Tine > > ##### > My sessionInfo: > >> sessionInfo() >> > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > other attached packages: > [1] hs133phsentrezgannot_1.1.0 GO_2.0.1 > hs133phsentrezgprobe_10.0.0 matchprobes_1.10.0 > [5] hs133phsentrezgcdf_10.0.0 AnnBuilder_1.16.0 > annotate_1.16.1 xtable_1.5-2 > [9] AnnotationDbi_1.0.6 RSQLite_0.6-4 > DBI_0.2-4 XML_1.93-2.1 > [13] affy_1.16.0 preprocessCore_1.0.0 > affyio_1.6.1 Biobase_1.16.2 > loaded via a namespace (and not attached): > [1] rcompgen_0.1-17 > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > # I did the following and got it to work: #1st I started with your code to put the IDs into a file. #(Please note that I am just assuming that what you are doing for this part is ok) library(AnnBuilder) library(hs133phsentrezgcdf) fN <- ls(hs133phsentrezgcdf) # to extract the featureNames in this CDF cfN <- sub("_at", "", fN) # to obtain the entrez gene IDs ## construct the base file mygeneNMap <- matrix(c(fN, cfN), byrow=F, ncol =2) write.table(mygeneNMap, file = "geneNMap", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE) mySrcUrls <- getSrcUrl("all", "Homo sapiens") #Your file of IDs looks like the right format for AnnBuilder at this point. #So I called ABPkgBuilder() like this: ABPkgBuilder(baseName="/home/mcarlson/tasks/tineke/geneNMap", srcUrls=mySrcUrls,baseMapType="ll",pkgName="chipFoo",pkgPath="/home/mc arlson/tasks/tineke",organism="Homo sapiens", version="1.0.0",author=list(author="Joe",maintainer="<joe.joe at="" gmail.com="">"),fromWeb = TRUE) #Here is my sessionInfo() Where I have made sure to try and use the same version of R... sessionInfo() R version 2.6.1 Patched (2008-01-09 r43930) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GO_2.0.1 hs133phsentrezgcdf_10.0.0 [3] AnnBuilder_1.16.0 annotate_1.16.1 [5] xtable_1.5-2 AnnotationDbi_1.0.6 [7] RSQLite_0.6-4 DBI_0.2-4 [9] XML_1.93-2 Biobase_1.16.2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 I hope this helps, Marc
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@groot-philip-de-1307
Last seen 8.2 years ago
Hello all, I missed this posting on the bioconductor mailing list. For several days now, email is no longer collected and submitted to me on 12 pm; I'll sent a seperate email on this problem later. Regarding your problem: I compiled and made available quite some annotation libraries for the Custom CDF files based on Entrez IDs. The authors of the Custom CDF-files are aware of this and promised me to inform the people whom need it, but apparently this is not always going well. Please download your annotation library here: http://nugo-r.bioinformatics.nl/NuGO_R.html <http: nugo-r.bioinformatics.nl="" nugo_r.html=""> If you have any question: just ask! Regards, Dr. Philip de Groot Wageningen University
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