question on library(mgu74av2.db) for SPIA package application
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Jing Huang ▴ 380
@jing-huang-4737
Last seen 7.2 years ago
Dear All members, I am using the library(mgu74av2.db), which is Affymetrix Murine Genome U74v2 annotation data (chip mgu74av2). I have an error message that I don’t understand. Could somebody advice me? Here is the R: library(SPIA) x=topTable(fit,coef="WThypo",n=1003) names(x) names(x) [1] "ID" "Gene.title" "Gene.symbol" [4] "Gene.ID" "UniGene.title" "UniGene.symbol" [7] "UniGene.ID" "Nucleotide.Title" "GI" [10] "GenBank.Accession" "Platform_CLONEID" "Platform_ORF" [13] "Platform_SPOTID" "Chromosome.location" "Chromosome.annotation" [16] "GO.Function" "GO.Process" "GO.Component" [19] "GO.Function.1" "GO.Process.1" "GO.Component.1" [22] "logFC" "AveExpr" "t" [25] "P.Value" "adj.P.Val" "B" library(mgu74av2.db) mgu74av2() y=mgu74av2ENTREZID x$ENTREZ=unlist(as.list(y[x$ID])) Error in as.list(y[x$ID]) : error in evaluating the argument 'x' in selecting a method for function 'as.list': Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs I have used the same set of scripts for other annotation packages and have not had any problem. Many many thanks Jing Oregon [[alternative HTML version deleted]]
Annotation Annotation • 565 views
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@freudenberg-johannes-nihniehs-e-4789
Last seen 7.2 years ago
Hi Jiang, It sounds like you have NAs in your ID list. Please check if > anyis.na(x$ID)) is TRUE. You could also the following as an alternative way to get the Entrez IDs: > x$ENTREZ <- toTable(mgu74av2ENTREZID)[match(x$ID, toTable(mgu74av2ENTREZID)[, 1]), 2] --Johannes -----Original Message----- From: Jing Huang [mailto:huangji@ohsu.edu] Sent: Wednesday, August 24, 2011 11:49 AM To: 'bioconductor at r-project.org' Subject: [BioC] question on library(mgu74av2.db) for SPIA package application Dear All members, I am using the library(mgu74av2.db), which is Affymetrix Murine Genome U74v2 annotation data (chip mgu74av2). I have an error message that I don???t understand. Could somebody advice me? Here is the R: library(SPIA) x=topTable(fit,coef="WThypo",n=1003) names(x) names(x) [1] "ID" "Gene.title" "Gene.symbol" [4] "Gene.ID" "UniGene.title" "UniGene.symbol" [7] "UniGene.ID" "Nucleotide.Title" "GI" [10] "GenBank.Accession" "Platform_CLONEID" "Platform_ORF" [13] "Platform_SPOTID" "Chromosome.location" "Chromosome.annotation" [16] "GO.Function" "GO.Process" "GO.Component" [19] "GO.Function.1" "GO.Process.1" "GO.Component.1" [22] "logFC" "AveExpr" "t" [25] "P.Value" "adj.P.Val" "B" library(mgu74av2.db) mgu74av2() y=mgu74av2ENTREZID x$ENTREZ=unlist(as.list(y[x$ID])) Error in as.list(y[x$ID]) : error in evaluating the argument 'x' in selecting a method for function 'as.list': Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs I have used the same set of scripts for other annotation packages and have not had any problem. Many many thanks Jing Oregon [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 21 hours ago
United States
Hi Jing, On 8/24/2011 11:48 AM, Jing Huang wrote: > Dear All members, > > I am using the library(mgu74av2.db), which is Affymetrix Murine Genome U74v2 annotation data (chip mgu74av2). I have an error message that I don???t understand. Could somebody advice me? > > Here is the R: > > library(SPIA) > x=topTable(fit,coef="WThypo",n=1003) > names(x) > > names(x) > [1] "ID" "Gene.title" "Gene.symbol" > [4] "Gene.ID" "UniGene.title" "UniGene.symbol" > [7] "UniGene.ID" "Nucleotide.Title" "GI" > [10] "GenBank.Accession" "Platform_CLONEID" "Platform_ORF" > [13] "Platform_SPOTID" "Chromosome.location" "Chromosome.annotation" > [16] "GO.Function" "GO.Process" "GO.Component" > [19] "GO.Function.1" "GO.Process.1" "GO.Component.1" > [22] "logFC" "AveExpr" "t" > [25] "P.Value" "adj.P.Val" "B" > > library(mgu74av2.db) > mgu74av2() > y=mgu74av2ENTREZID > x$ENTREZ=unlist(as.list(y[x$ID])) > > Error in as.list(y[x$ID]) : > error in evaluating the argument 'x' in selecting a method for function 'as.list': Error in .checkKeysAreWellFormed(keys) : > keys must be supplied in a character vector with no NAs The above error is saying that your x$ID vector contains NA values. You need to subset out the NAs first. Best, Jim > > I have used the same set of scripts for other annotation packages and have not had any problem. > > Many many thanks > > Jing > > Oregon > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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