Hi, Lina, We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to support Gallus gallus (taxon id 9031). You can get it from svn right away or wait 2 days to download it from bioc website. Or if you want to try it now, here is the changes: ================================================================ --- IPI.R (new) +++ IPI.R (old) @@ -21,8 +21,7 @@ speciesNorganismTable <- rbind( c("human", "Homo sapiens"), c("mouse", "Mus musculus"), - c("rat", "Rattus norvegicus"), - c("chick", "Gallus gallus") + c("rat", "Rattus norvegicus") ) colnames(speciesNorganismTable) <- c("species", "organism") return(speciesNorganismTable) ================================================================= The above change happens in function "speciesNorganism". This allows you get annotation for PFAM and PROSITE. ================================================================= --- getSrcUrl.R (new) +++ getSrcUrl.R (old) @@ -65,7 +65,6 @@ "DANIO RERIO" = "Danio_Rerio", "CAENORHABDITIS ELEGANS" = "Caenorhabditis_elegans", "DROSOPHILA MELANOGASTER" = "Drosophila_melanogaster", - "GALLUS GALLUS" = "Gallus_gallus", NA) ifis.na(key)) { warning(paste("Organism", organism, "is not supported by GoldenPath (GP).")) @@ -170,7 +169,6 @@ Sma = "Schistosoma mansoni", Ssa = "Salmo salar", Ssc = "Sus scrofa", Str = "Xenopus tropicalis", Xl = "Xenopus laevis", At = "Arabidopsis thaliana", - Gga = "Gallus gallus", Gma = "Glycine max", Han = "Helianthus annus", Hv = "Hordeum vulgare", Lsa = " Lactuca sativa", Les = "Lycopersicon esculentum", Lco = "Lotus corniculatus", ================================================================== The first change is in function "getUCSCUrl", for chromosome location. The second is in function "UGSciNames" for UniGene. I test it with this script: =============================== library(AnnBuilder) mypkg <- function(pkgPath, version) { ABPkgBuilder(baseName="mybase.txt", baseMapType="ll", pkgName="mypkg", pkgPath=pkgPath, organism="Gallus gallus", version=version, author=list( authors="Nianhua Li", maintainer="Nianhua Li<email at="" email.org="">" ) ) } mypkg(getwd(), "1.0.0") =============================== mybase.txt is 1 395929 2 395844 3 396017 4 415357 5 424377 QC data is: Number of probes: 5 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 5 mypkgCHRLOC found 4 of 5 mypkgCHR found 5 of 5 mypkgENZYME found 4 of 5 mypkgGENENAME found 0 of 5 mypkgGO found 5 of 5 mypkgLOCUSID found 5 of 5 mypkgMAP found 0 of 5 mypkgPATH found 5 of 5 mypkgPMID found 3 of 5 mypkgREFSEQ found 5 of 5 mypkgSUMFUNC found 0 of 5 mypkgSYMBOL found 5 of 5 mypkgUNIGENE found 5 of 5 Mappings found for non-probe based rda files: mypkgENZYME2PROBE found 5 mypkgGO2ALLPROBES found 107 mypkgGO2PROBE found 19 mypkgORGANISM found 1 mypkgPATH2PROBE found 18 mypkgPFAM found 5 mypkgPMID2PROBE found 4 mypkgPROSITE found 3 Let me know if you have any questions or concerns. Cheers! nianhua

Hi Jim and Nianhua! Thank you so much for your answers, perfect timing that the new AnnBuilder version will support chicken!! Yes Jim, my goal is to output a list of the top probesets along with annotations as well as to be able to add gene names to volcano plots etc. And later on also perhaps use the functional annotations, like GO, for some analyses. I have quite a lot of annotation data in the annotation file provided by affymetrix - mappings to different identifiers, functional annotations etc. I might have everything I need there but I don't know how to "connect" that to my affybatch or exprSet object or output from limma to handle it easily. Thanks again! Best, Lina -----Ursprungligt meddelande----- Fr?n: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] F?r Nianhua Li Skickat: den 17 augusti 2006 03:15 Till: bioconductor at stat.math.ethz.ch ?mne: Re: [BioC] annotation package for chicken affyprobes Hi, Lina, We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to support Gallus gallus (taxon id 9031). You can get it from svn right away or wait 2 days to download it from bioc website. Or if you want to try it now, here is the changes: ================================================================ --- IPI.R (new) +++ IPI.R (old) @@ -21,8 +21,7 @@ speciesNorganismTable <- rbind( c("human", "Homo sapiens"), c("mouse", "Mus musculus"), - c("rat", "Rattus norvegicus"), - c("chick", "Gallus gallus") + c("rat", "Rattus norvegicus") ) colnames(speciesNorganismTable) <- c("species", "organism") return(speciesNorganismTable) ================================================================= The above change happens in function "speciesNorganism". This allows you get annotation for PFAM and PROSITE. ================================================================= --- getSrcUrl.R (new) +++ getSrcUrl.R (old) @@ -65,7 +65,6 @@ "DANIO RERIO" = "Danio_Rerio", "CAENORHABDITIS ELEGANS" = "Caenorhabditis_elegans", "DROSOPHILA MELANOGASTER" = "Drosophila_melanogaster", - "GALLUS GALLUS" = "Gallus_gallus", NA) ifis.na(key)) { warning(paste("Organism", organism, "is not supported by GoldenPath (GP).")) @@ -170,7 +169,6 @@ Sma = "Schistosoma mansoni", Ssa = "Salmo salar", Ssc = "Sus scrofa", Str = "Xenopus tropicalis", Xl = "Xenopus laevis", At = "Arabidopsis thaliana", - Gga = "Gallus gallus", Gma = "Glycine max", Han = "Helianthus annus", Hv = "Hordeum vulgare", Lsa = " Lactuca sativa", Les = "Lycopersicon esculentum", Lco = "Lotus corniculatus", ================================================================== The first change is in function "getUCSCUrl", for chromosome location. The second is in function "UGSciNames" for UniGene. I test it with this script: =============================== library(AnnBuilder) mypkg <- function(pkgPath, version) { ABPkgBuilder(baseName="mybase.txt", baseMapType="ll", pkgName="mypkg", pkgPath=pkgPath, organism="Gallus gallus", version=version, author=list( authors="Nianhua Li", maintainer="Nianhua Li<email at="" email.org="">" ) ) } mypkg(getwd(), "1.0.0") =============================== mybase.txt is 1 395929 2 395844 3 396017 4 415357 5 424377 QC data is: Number of probes: 5 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 5 mypkgCHRLOC found 4 of 5 mypkgCHR found 5 of 5 mypkgENZYME found 4 of 5 mypkgGENENAME found 0 of 5 mypkgGO found 5 of 5 mypkgLOCUSID found 5 of 5 mypkgMAP found 0 of 5 mypkgPATH found 5 of 5 mypkgPMID found 3 of 5 mypkgREFSEQ found 5 of 5 mypkgSUMFUNC found 0 of 5 mypkgSYMBOL found 5 of 5 mypkgUNIGENE found 5 of 5 Mappings found for non-probe based rda files: mypkgENZYME2PROBE found 5 mypkgGO2ALLPROBES found 107 mypkgGO2PROBE found 19 mypkgORGANISM found 1 mypkgPATH2PROBE found 18 mypkgPFAM found 5 mypkgPMID2PROBE found 4 mypkgPROSITE found 3 Let me know if you have any questions or concerns. Cheers! nianhua _______________________________________________ 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 again Nianhua! I have now installed the new version of AnnBuilder (1.11.8) and wanted to try it with your test script and test file below before I did any attempt to build the package for chicken. I created the mybase.txt and ran the script but got the following error/warning messages: ______________________________________________________________________ ___ Error in "[.data.frame"(temp, , 2) : undefined columns selected In addition: Warning message: data length [5] is not a sub-multiple or multiple of the number of rows [3] in matrix ______________________________________________________________________ ____ Might be something simple I did wrong but can't really figure it out myself. Do you know what might be the problem? Thank you! /Lina -----Ursprungligt meddelande----- Fr?n: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] F?r Nianhua Li Skickat: den 17 augusti 2006 03:15 Till: bioconductor at stat.math.ethz.ch ?mne: Re: [BioC] annotation package for chicken affyprobes Hi, Lina, We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to support Gallus gallus (taxon id 9031). You can get it from svn right away or wait 2 days to download it from bioc website. Or if you want to try it now, here is the changes: ================================================================ --- IPI.R (new) +++ IPI.R (old) @@ -21,8 +21,7 @@ speciesNorganismTable <- rbind( c("human", "Homo sapiens"), c("mouse", "Mus musculus"), - c("rat", "Rattus norvegicus"), - c("chick", "Gallus gallus") + c("rat", "Rattus norvegicus") ) colnames(speciesNorganismTable) <- c("species", "organism") return(speciesNorganismTable) ================================================================= The above change happens in function "speciesNorganism". This allows you get annotation for PFAM and PROSITE. ================================================================= --- getSrcUrl.R (new) +++ getSrcUrl.R (old) @@ -65,7 +65,6 @@ "DANIO RERIO" = "Danio_Rerio", "CAENORHABDITIS ELEGANS" = "Caenorhabditis_elegans", "DROSOPHILA MELANOGASTER" = "Drosophila_melanogaster", - "GALLUS GALLUS" = "Gallus_gallus", NA) ifis.na(key)) { warning(paste("Organism", organism, "is not supported by GoldenPath (GP).")) @@ -170,7 +169,6 @@ Sma = "Schistosoma mansoni", Ssa = "Salmo salar", Ssc = "Sus scrofa", Str = "Xenopus tropicalis", Xl = "Xenopus laevis", At = "Arabidopsis thaliana", - Gga = "Gallus gallus", Gma = "Glycine max", Han = "Helianthus annus", Hv = "Hordeum vulgare", Lsa = " Lactuca sativa", Les = "Lycopersicon esculentum", Lco = "Lotus corniculatus", ================================================================== The first change is in function "getUCSCUrl", for chromosome location. The second is in function "UGSciNames" for UniGene. I test it with this script: =============================== library(AnnBuilder) mypkg <- function(pkgPath, version) { ABPkgBuilder(baseName="mybase.txt", baseMapType="ll", pkgName="mypkg", pkgPath=pkgPath, organism="Gallus gallus", version=version, author=list( authors="Nianhua Li", maintainer="Nianhua Li<email at="" email.org="">" ) ) } mypkg(getwd(), "1.0.0") =============================== mybase.txt is 1 395929 2 395844 3 396017 4 415357 5 424377 QC data is: Number of probes: 5 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 5 mypkgCHRLOC found 4 of 5 mypkgCHR found 5 of 5 mypkgENZYME found 4 of 5 mypkgGENENAME found 0 of 5 mypkgGO found 5 of 5 mypkgLOCUSID found 5 of 5 mypkgMAP found 0 of 5 mypkgPATH found 5 of 5 mypkgPMID found 3 of 5 mypkgREFSEQ found 5 of 5 mypkgSUMFUNC found 0 of 5 mypkgSYMBOL found 5 of 5 mypkgUNIGENE found 5 of 5 Mappings found for non-probe based rda files: mypkgENZYME2PROBE found 5 mypkgGO2ALLPROBES found 107 mypkgGO2PROBE found 19 mypkgORGANISM found 1 mypkgPATH2PROBE found 18 mypkgPFAM found 5 mypkgPMID2PROBE found 4 mypkgPROSITE found 3 Let me know if you have any questions or concerns. Cheers! nianhua _______________________________________________ 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 again! I managed to build the annotation package for chicken - thanks for all your help! I was a bit surprised though by the low annotation coverage, see QC data below. I don't really know how the data is collected but I would think more information on chromosome location is known for the probesets. When reading about the new chicken genome assembly (http://genome.ucsc.edu) it says that around 95% of the sequence has been anchored to chromosomes. I thought the annotation process in R used this information? What can be the reason for the very few anchored probesets? I might be doing something wrong or perhaps it is a problem of mapping probe id's to other identifiers? I used the genbank mappings as mybasefile and unigene and entrez mappings as other sources. Is there a way within R to increase annotation coverage? I am especially interested in chromosome location (number), but maybe this is a problem that is best solved outside R? Would greatly appreciate some help! Thank you, Lina ====================================================================== = QC data: Number of probes: 38535 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: chickenACCNUM found 25654 of 38535 chickenCHR found 9707 of 38535 chickenCHRLOC found 156 of 38535 chickenENZYME found 52 of 38535 chickenGENENAME found 0 of 38535 chickenGO found 4224 of 38535 chickenLOCUSID found 9722 of 38535 chickenMAP found 0 of 38535 chickenPATH found 87 of 38535 chickenPMID found 283 of 38535 chickenREFSEQ found 9709 of 38535 chickenSUMFUNC found 0 of 38535 chickenSYMBOL found 9722 of 38535 chickenUNIGENE found 289 of 38535 Mappings found for non-probe based rda files: chickenENZYME2PROBE found 33 chickenGO2ALLPROBES found 1785 chickenGO2PROBE found 930 chickenORGANISM found 1 chickenPATH2PROBE found 31 chickenPFAM found 7418 chickenPMID2PROBE found 101 chickenPROSITE found 5490 ====================================================================== ==== -----Ursprungligt meddelande----- Fr?n: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] F?r Nianhua Li Skickat: den 17 augusti 2006 03:15 Till: bioconductor at stat.math.ethz.ch ?mne: Re: [BioC] annotation package for chicken affyprobes Hi, Lina, We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to support Gallus gallus (taxon id 9031). You can get it from svn right away or wait 2 days to download it from bioc website. Or if you want to try it now, here is the changes: ================================================================ --- IPI.R (new) +++ IPI.R (old) @@ -21,8 +21,7 @@ speciesNorganismTable <- rbind( c("human", "Homo sapiens"), c("mouse", "Mus musculus"), - c("rat", "Rattus norvegicus"), - c("chick", "Gallus gallus") + c("rat", "Rattus norvegicus") ) colnames(speciesNorganismTable) <- c("species", "organism") return(speciesNorganismTable) ================================================================= The above change happens in function "speciesNorganism". This allows you get annotation for PFAM and PROSITE. ================================================================= --- getSrcUrl.R (new) +++ getSrcUrl.R (old) @@ -65,7 +65,6 @@ "DANIO RERIO" = "Danio_Rerio", "CAENORHABDITIS ELEGANS" = "Caenorhabditis_elegans", "DROSOPHILA MELANOGASTER" = "Drosophila_melanogaster", - "GALLUS GALLUS" = "Gallus_gallus", NA) ifis.na(key)) { warning(paste("Organism", organism, "is not supported by GoldenPath (GP).")) @@ -170,7 +169,6 @@ Sma = "Schistosoma mansoni", Ssa = "Salmo salar", Ssc = "Sus scrofa", Str = "Xenopus tropicalis", Xl = "Xenopus laevis", At = "Arabidopsis thaliana", - Gga = "Gallus gallus", Gma = "Glycine max", Han = "Helianthus annus", Hv = "Hordeum vulgare", Lsa = " Lactuca sativa", Les = "Lycopersicon esculentum", Lco = "Lotus corniculatus", ================================================================== The first change is in function "getUCSCUrl", for chromosome location. The second is in function "UGSciNames" for UniGene. I test it with this script: =============================== library(AnnBuilder) mypkg <- function(pkgPath, version) { ABPkgBuilder(baseName="mybase.txt", baseMapType="ll", pkgName="mypkg", pkgPath=pkgPath, organism="Gallus gallus", version=version, author=list( authors="Nianhua Li", maintainer="Nianhua Li<email at="" email.org="">" ) ) } mypkg(getwd(), "1.0.0") =============================== mybase.txt is 1 395929 2 395844 3 396017 4 415357 5 424377 QC data is: Number of probes: 5 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 5 mypkgCHRLOC found 4 of 5 mypkgCHR found 5 of 5 mypkgENZYME found 4 of 5 mypkgGENENAME found 0 of 5 mypkgGO found 5 of 5 mypkgLOCUSID found 5 of 5 mypkgMAP found 0 of 5 mypkgPATH found 5 of 5 mypkgPMID found 3 of 5 mypkgREFSEQ found 5 of 5 mypkgSUMFUNC found 0 of 5 mypkgSYMBOL found 5 of 5 mypkgUNIGENE found 5 of 5 Mappings found for non-probe based rda files: mypkgENZYME2PROBE found 5 mypkgGO2ALLPROBES found 107 mypkgGO2PROBE found 19 mypkgORGANISM found 1 mypkgPATH2PROBE found 18 mypkgPFAM found 5 mypkgPMID2PROBE found 4 mypkgPROSITE found 3 Let me know if you have any questions or concerns. Cheers! nianhua _______________________________________________ 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