trouble with yeastann function in AnnBuilder
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@jacob-michaelson-1079
Last seen 9.6 years ago
I think I finally found what I need to build a decent Yeast 2.0 annotation package, but unfortunately, I keep getting errors. The base file needed for yeastann is a two-column matrix containing probe ids and SGD accession numbers. I created such a file by whittling down Affymetrix's Yeast 2.0 CSV annotation file into those two columns. From the AnnBuilder documentation for yeastann: Arguments base base a matrix with two columns. The first column is probe ids and the second one are the mappings to SGD ids used by all the Yeast Genome data files. If base = "", the whole genome will be mapped based on a data file that contains mappings between all the ORFs and SGD ids I then imported the above file into R using: > yeastsgd=read.csv("yeastsgd.csv") and then > yeastsgd=as.matrix(yeastsgd) ...just to be safe (although I also tried without and still got errors). Then I pasted the default function from the yeastann documentation, substituting my yeastsgd matrix into the base =" " position as follows: yeastAnn(base = yeastsgd, yGenoUrl = + "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/", + yGenoNames = + c("literature_curation/gene_literature.tab", + "chromosomal_feature/SGD_features.tab", + "literature_curation/gene_association.sgd"), toKeep = + list(c(6, 1), c(9, 2, 5, 6, 8, 11, 3), c(2, 5, 7)), + colNames = list(c("sgdid", "pmid"), c("sgdid", + "genename", "chr", "chrloc", "chrori", "description", + "alias"), c("sgdid", "go")), seps = c("\t", "\t", + "\t"), by = "sgdid") which immediately produced the error message (FYI in the "base" position I tried both with and without quotes, both of which produced errors): Error in file(file, "r") : unable to open connection In addition: Warning messages: 1: the condition has length > 1 and only the first element will be used in: if (probe2ORF == "") { 2: only first element of `description' argument used 3: cannot open file `1769308_at' I'm not sure why it keeps misunderstanding a matrix when the documentation specifically calls for a matrix (for some reason it thinks 1769308_at is a file and not a probe). I verified that the imported data contains the data in the proper placement, which it does, and the dimensions seem to be correct: > dim(yeastsgd) [1] 10928 2 Also FYI here's the error message when the above yeastann function is implemented and yeastsgd is imported using read.csv, but not as.matrix: Error in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white = TRUE) : argument 'file' must be a character string or connection In addition: Warning message: the condition has length > 1 and only the first element will be used in: if (probe2ORF == "") { I'd really appreciate any help or suggestions. Thanks! --Jake Michaelson [[alternative text/enriched version deleted]]
Annotation Yeast probe AnnBuilder safe Annotation Yeast probe AnnBuilder safe • 1.0k views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Jacob Michaelson wrote: > I think I finally found what I need to build a decent Yeast 2.0 > annotation package, but unfortunately, I keep getting errors. > > The base file needed for yeastann is a two-column matrix containing > probe ids and SGD accession numbers. I created such a file by > whittling down Affymetrix's Yeast 2.0 CSV annotation file into those > two columns. > > From the AnnBuilder documentation for yeastann: > > Arguments > > base > base a matrix with two columns. The first column is probe ids and the > second one are the mappings to SGD ids used by all the Yeast Genome > data files. If base = "", the whole genome will be mapped based on a > data file that contains mappings between all the ORFs and SGD ids Although it states here that base is supposed to be a matrix with two columns, really what it is supposed to be is a _file_ containing a matrix with two columns. The file should be in your working directory. > > I then imported the above file into R using: > > > yeastsgd=read.csv("yeastsgd.csv") > > and then > > > yeastsgd=as.matrix(yeastsgd) > > ...just to be safe (although I also tried without and still got errors). > > Then I pasted the default function from the yeastann documentation, > substituting my yeastsgd matrix into the base =" " position as follows: > > yeastAnn(base = yeastsgd, yGenoUrl = > + > "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/", > + yGenoNames = > + c("literature_curation/gene_literature.tab", > + "chromosomal_feature/SGD_features.tab", > + "literature_curation/gene_association.sgd"), toKeep = > + list(c(6, 1), c(9, 2, 5, 6, 8, 11, 3), c(2, 5, 7)), > + colNames = list(c("sgdid", "pmid"), c("sgdid", > + "genename", "chr", "chrloc", "chrori", "description", > + "alias"), c("sgdid", "go")), seps = c("\t", "\t", > + "\t"), by = "sgdid") > > which immediately produced the error message (FYI in the "base" > position I tried both with and without quotes, both of which produced > errors): > > Error in file(file, "r") : unable to open connection > In addition: Warning messages: > 1: the condition has length > 1 and only the first element will be used > in: if (probe2ORF == "") { > 2: only first element of `description' argument used > 3: cannot open file `1769308_at' > > I'm not sure why it keeps misunderstanding a matrix when the > documentation specifically calls for a matrix (for some reason it > thinks 1769308_at is a file and not a probe). > > I verified that the imported data contains the data in the proper > placement, which it does, and the dimensions seem to be correct: > > > dim(yeastsgd) > [1] 10928 2 > > Also FYI here's the error message when the above yeastann function is > implemented and yeastsgd is imported using read.csv, but not as.matrix: > > Error in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white > = TRUE) : > argument 'file' must be a character string or connection > In addition: Warning message: > the condition has length > 1 and only the first element will be used > in: if (probe2ORF == "") { So this error is basically saying that R looked for the file 'yeastsgd' in the current working directory, and couldn't find it. HTH, Jim > > I'd really appreciate any help or suggestions. > > Thanks! > > --Jake Michaelson > > [[alternative text/enriched version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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John Zhang ▴ 10
@john-zhang-1098
Last seen 9.6 years ago
Sorry, I forgot to update the man page. base should be a file name. If you would like to build a annotation package, yeastPkgBuilder is the correct function to use. Thanks. >X-Original-To: jzhang@jimmy.harvard.edu >Delivered-To: jzhang@jimmy.harvard.edu >Mime-Version: 1.0 (Apple Message framework v619.2) >To: bioconductor@stat.math.ethz.ch >From: Jacob Michaelson <jjmichael@comcast.net> >Date: Wed, 2 Feb 2005 19:06:52 -0700 >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of jjmichael@comcast.net does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Content-Disposition: inline >Content-Transfer-Encoding: 7bit >Subject: [BioC] trouble with yeastann function in AnnBuilder >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.5 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=0.1 required=3.0 tests=FORGED_RCVD_HELO autolearn=ham version=3.0.1 > >I think I finally found what I need to build a decent Yeast 2.0 >annotation package, but unfortunately, I keep getting errors. > >The base file needed for yeastann is a two-column matrix containing >probe ids and SGD accession numbers. I created such a file by >whittling down Affymetrix's Yeast 2.0 CSV annotation file into those >two columns. > > From the AnnBuilder documentation for yeastann: > >Arguments > >base >base a matrix with two columns. The first column is probe ids and the >second one are the mappings to SGD ids used by all the Yeast Genome >data files. If base = "", the whole genome will be mapped based on a >data file that contains mappings between all the ORFs and SGD ids > >I then imported the above file into R using: > > > yeastsgd=read.csv("yeastsgd.csv") > >and then > > > yeastsgd=as.matrix(yeastsgd) > >...just to be safe (although I also tried without and still got errors). > >Then I pasted the default function from the yeastann documentation, >substituting my yeastsgd matrix into the base =" " position as follows: > >yeastAnn(base = yeastsgd, yGenoUrl = >+ >"ftp://genome-ftp.stanford.edu/pub/yeast/data_download/", >+ yGenoNames = >+ c("literature_curation/gene_literature.tab", >+ "chromosomal_feature/SGD_features.tab", >+ "literature_curation/gene_association.sgd"), toKeep = >+ list(c(6, 1), c(9, 2, 5, 6, 8, 11, 3), c(2, 5, 7)), >+ colNames = list(c("sgdid", "pmid"), c("sgdid", >+ "genename", "chr", "chrloc", "chrori", "description", >+ "alias"), c("sgdid", "go")), seps = c("\t", "\t", >+ "\t"), by = "sgdid") > >which immediately produced the error message (FYI in the "base" >position I tried both with and without quotes, both of which produced >errors): > >Error in file(file, "r") : unable to open connection >In addition: Warning messages: >1: the condition has length > 1 and only the first element will be used >in: if (probe2ORF == "") { >2: only first element of `description' argument used >3: cannot open file `1769308_at' > >I'm not sure why it keeps misunderstanding a matrix when the >documentation specifically calls for a matrix (for some reason it >thinks 1769308_at is a file and not a probe). > >I verified that the imported data contains the data in the proper >placement, which it does, and the dimensions seem to be correct: > > > dim(yeastsgd) >[1] 10928 2 > >Also FYI here's the error message when the above yeastann function is >implemented and yeastsgd is imported using read.csv, but not as.matrix: > >Error in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white >= TRUE) : > argument 'file' must be a character string or connection >In addition: Warning message: >the condition has length > 1 and only the first element will be used >in: if (probe2ORF == "") { > >I'd really appreciate any help or suggestions. > >Thanks! > >--Jake Michaelson > > [[alternative text/enriched version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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