Hi Alice, Using your code, I get the following results: > a <- c("1397882_at", "1394539_at", "1397115_at", "1369569_at", "1389862_at", "1383230_at", "1389175_at", "1372644_at", "1378579_at", "1375210_at", "1398872_at", "1371842_at", "1392240_at", "1369133_a_at", "1370123_a_at", "1395529_at", "1398185_at", "1384220_at", "1387589_at", "1373634_at", "1376280_at", "1379569_at", "1396519_at", "1372832_at", "1368260_at", "1372145_at", "1382644_at", "1388579_at", "1385210_at", "1381842_at", "1374624_at", "1376349_a_at", "1373822_at", "1394220_at", "1397589_at", "1369250_at") > b <- c("313049", "64572", "360937", "65140", "362955", "360664", "305455", "686765", NA, NA, "161477", "679898", NA, "117101", "60465", NA, "306424", "316221", "65025", NA, NA, NA, "24418", NA, "114592", "294810", NA, "689414", "305987", "293024", "311952", "65194", "303740", "316012", NA, "116642", "619440", "300446", "366792", "294799", "688699", "298594", "24172", "303787", NA, "114561", "305895", "498331", "361256", NA) These are different lengths, so > write.table(cbind(a, b[1:36]), "myBase", quote=F, sep="\t", col.names=F, row.names=F) > mySrcUrls <- getSrcUrl("all", "Rattus norvegicus") > ABPkgBuilder(baseName="myBase", srcUrls=mySrcUrls, baseMapType="ll", pkgName="rats", organism="Rattus norvegicus", version="0.0.1", pkgPath=getwd(), author=list(authors="me", maintainer="me <me at="" mine.com="">"), fromWeb=TRUE) [snip] Then I installed using R CMD INSTALL > library(rats) > rats() Quality control information for rats Date built: Created: Wed Nov 14 12:06:00 2007 Number of probes: 36 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: ratsACCNUM found 0 of 36 ratsCHR found 26 of 36 ratsCHRLOC found 20 of 36 ratsENTREZID found 26 of 36 ratsENZYME found 0 of 36 ratsGENENAME found 26 of 36 ratsGO found 20 of 36 ratsMAP found 25 of 36 ratsPATH found 0 of 36 ratsPMID found 17 of 36 ratsREFSEQ found 26 of 36 ratsSUMFUNC found 0 of 36 ratsSYMBOL found 26 of 36 ratsUNIGENE found 23 of 36 Mappings found for non-probe based rda files: ratsCHRLENGTHS found 21 ratsGO.1 found 0 ratsGO2ALLPROBES found 345 ratsGO2PROBE found 106 ratsORGANISM found 1 ratsPFAM found 18 ratsPMID2PROBE found 94 ratsPROSITE found 14 > sessionInfo() R version 2.6.0 beta (2007-09-24 r42966) 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] stats graphics grDevices datasets utils methods base other attached packages: [1] rats_0.0.1 rcompgen_0.1-15 loaded via a namespace (and not attached): [1] Biobase_1.16.0 tools_2.6.0 Best, Jim Johnstone, Alice wrote: > It is the code in the vignette that I have been following (ABPrimer) .. > Although when I try this exactly using the example base file I still get > the following error > >> ABPkgBuilder(baseName = "myBase", srcUrls = mySrcUrls, baseMapType = > + myBaseType, pkgName = "hgu95av2", > + pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", > + author = list(authors = "myname", maintainer = > + "myname at myemail.com"), fromWeb = TRUE) > Error in getBaseFile(baseName) : > Base file myBase may not be valid or have two columns > > -----Original Message----- > From: Marc Carlson [mailto:mcarlson at fhcrc.org] > Sent: Wednesday, 14 November 2007 2:37 p.m. > To: Johnstone, Alice > Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Help with base file in AnnBuilder > > Johnstone, Alice wrote: >> Hi Marc, >> This doesn't seem to be the problem as its an object so doesn't need >> the quotes in the ABPkgBuilder command. Adding quotes and calling it >> in the command itself doesn't fix the problem either.. >> >> -----Original Message----- >> From: Marc Carlson [mailto:mcarlson at fhcrc.org] >> Sent: Wednesday, 14 November 2007 12:46 p.m. >> To: Johnstone, Alice >> Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Help with base file in AnnBuilder >> >> Johnstone, Alice wrote: >> >>> My data file was in a tab-separated file, how do you read it without >>> it reading as a data.frame or matrix? >>> >>> -----Original Message----- >>> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] >>> Sent: Wednesday, 14 November 2007 11:30 a.m. >>> To: Johnstone, Alice >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Help with base file in AnnBuilder >>> >>> Hi Alice, >>> >>> Johnstone, Alice wrote: >>> >>> >>>> Hi >>>> I have been trying to create a annotation package but have become >>>> stuck with my base file. I am not sure what format it needs to be >>>> >> in. >> >>>> >>>> >>> >>> >>>> Also could someone clarify what a "map" is? Ie what the help files >>>> ask >>>> >>>> >>> >>> >>>> for to be in the second column of the base file, is this just the >>>> accession numbers, genebank ids etc? (from the helpfile "the second >>>> one being the maps to GenBank accession numbers")? >>>> >>>> >>> The base file is supposed to be a tab-separated _text file_ that >>> contains the (in this case) Affy IDs in the first column, and the >>> Entrez Gene IDs in the second. It appears here that you are using >>> either a matrix or a data.frame. >>> >>> Does it work if you first do something like >>> >>> write.table(myBase, "myBase", sep="\t", col.names=FALSE, >>> row.names=FALSE) >>> >>> and then try again using >>> >>> ABPkgBuilder(baseName="myBase", <otherargshere>)? >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> >>>>> ABPkgBuilder(baseName=myBase,srcUrls=mySrcUrls,baseMapType="ll", >>>>> >>>>> >>>> + pkgName="rats",pkgPath=myDir,organism="Rattus >>>> norvegicus",version="1.1.0", >>>> + >>>> author=list(authors="Alice",maintainer="alice.johnstone at esr.cri.nz") >>>> , >>>> f >>>> ro >>>> mWeb=TRUE) >>>> Error in getBaseFile(baseName) : >>>> Base file c("1397882_at", "1394539_at", "1397115_at", >>>> "1369569_at", >>>> >> >>>> "1389862_at", "1383230_at", "1389175_at", "1372644_at", >>>> "1378579_at", >>>> >> >>>> "1375210_at", "1398872_at", "1371842_at", "1392240_at", >>>> "1369133_a_at", "1370123_a_at", "1395529_at", "1398185_at", >>>> "1384220_at", "1387589_at", "1373634_at", "1376280_at", >>>> "1379569_at", >>>> >> >>>> "1396519_at", "1372832_at", "1368260_at", "1372145_at", >>>> "1382644_at", >>>> >> >>>> "1388579_at", "1385210_at", "1381842_at", "1374624_at", >>>> "1376349_a_at", "1373822_at", "1394220_at", "1397589_at", >>>> "1369250_at", may not be valid or have two columnsBase file >>>> c("313049", "64572", "360937", "65140", "362955", "360664", >>>> "305455", >>>> >> >>>> "686765", NA, NA, "161477", "679898", NA, "117101", "60465", NA, >>>> "306424", "316221", "65025", NA, NA, NA, "24418", NA, "114592", >>>> "294810", NA, "689414", "305987", "293024", "311952", "65194", >>>> "303740", "316012", NA, "116642", "619440", "300446", "366792", >>>> "294799", "688699", "298594", "24172", "303787", NA, "114561", >>>> "305895", "498331", "361256", NA >>>> >>>> >>>>> traceback() >>>>> >>>>> >>>> 4: stop(paste("Base file", baseName, "may not be valid or have two >>>> columns")) >>>> 3: getBaseFile(baseName) >>>> 2: getUniMappings(baseName, srcObjs[["eg"]], srcObjs[["ug"]], NULL, >>>> baseMapType) >>>> 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType >>>> = >>>> >> >>>> "ll", >>>> pkgName = "rats", pkgPath = myDir, organism = "Rattus >>>> norvegicus", >>>> version = "1.1.0", author = list(authors = "Alice", >>>> maintainer >>>> >> >>>> = "alice.johnstone at esr.cri.nz"), >>>> fromWeb = TRUE) >>>> >>>> >>>>> str(myBase) >>>>> >>>>> >>>> 'data.frame': 53622 obs. of 2 variables: >>>> $ V1: chr "1397882_at" "1394539_at" "1397115_at" "1369569_at" ... >>>> $ V2: chr "313049" "64572" "360937" "65140" ... >>>> >>>> >>>>> sessionInfo() >>>>> >>>>> >>>> R version 2.7.0 Under development (unstable) (2007-11-10 r43420) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New >>>> Zealand.1252;LC_MONETARY=English_New >>>> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils datasets >>>> >>>> >>> methods >>> >>> >>>> base >>>> >>>> other attached packages: >>>> [1] GO_2.0.1 lumiRatV1_1.3.1 rat2302_2.0.1 >>>> AnnBuilder_1.17.0 annotate_1.17.2 >>>> [6] xtable_1.5-2 AnnotationDbi_1.1.6 RSQLite_0.6-4 >>>> DBI_0.2-4 XML_1.9-0 >>>> [11] Biobase_1.17.4 >>>> >>>> >>>> >>>> Alice Johnstone >>>> >>>> PhD Student >>>> Institute of Environmental Science and Research Ltd Kenepuru Science > >>>> Centre >>>> 34 Kenepuru Drive >>>> PO Box 50-348 >>>> Porirua >>>> New Zealand >>>> >>>> Tel: + 64 4 914-0717 >>>> Fax: + 64 4 914-0770 >>>> >>>> >>>> P Think before you print >>>> This e-mail transmission and any attachments that accompany it may >>>> >>>> >>> contain information that is privileged, confidential or otherwise >>> exempt from disclosure under applicable law and is intended solely >>> for >>> >> >>> the use of the individual(s) to whom it was intended to be addressed. >>> >>> >>>> If you have received this e-mail by mistake, or you are not the >>>> >>>> >>> intended recipient, any disclosure, dissemination, distribution, >>> copying or other use or retention of this communication or its >>> substance is prohibited. If you have received this communication in >>> error, please immediately reply to the author via e-mail that you >>> received this message by mistake and also permanently delete the >>> original and all copies of this e-mail and any attachments from your >>> >> computer. Thank you. >> >>> >>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Affymetrix and cDNA Microarray Core >>> University of Michigan Cancer Center >>> 1500 E. Medical Center Drive >>> 7410 CCGC >>> Ann Arbor MI 48109 >>> 734-647-5623 >>> >>> _______________________________________________ >>> 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 Alice, >> >> >From reading your two posts I think that all you are missing might >>> just >> be the quotes around the filename that you are trying to pass in? >> >> Marc > > Yes well it's not supposed to be an R object. It needs to be a > tab-delimited file instead. > > James had a good suggestion for you to write your object back out to a > file so that you could then feed that file to the function. > > > Have you seen that there is documentation for AnnBuilder located on this > page? > > http://bioconductor.org/packages/2.1/bioc/html/AnnBuilder.html > > > hope this helps you, > > > Marc -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623