Help with base file in AnnBuilder
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@johnstone-alice-2290
Last seen 9.6 years ago
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")? > 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"),fro 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.
Annotation Organism Annotation Organism • 1.2k views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States
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"),fro > 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
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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@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
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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
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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@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
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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
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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@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
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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
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Entering edit mode
Hi Alice, If you can type something like ABPkgBuilder(baseName=myBase, ...) then what is being picked up by R is an object in the global workspace with that name rather than a text file. For it to find a text file you will have to pass a character string (hence the quotation marks). Best, Jim 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 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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