Hi All, I am getting a strange error converting Gene Symbols to Entrez ID. Here is my code: >testData = read.delim("IL_CellVar.txt",head=T,row.names = 2) > testData[1:5,1:3] ClustID Genes.Symbol ChrLoc NM_001034168.1 4 Ank2 chrNA:-1--1 NM_013795.4 4 Atp5l chrNA:-1--1 NM_018770 4 Igsf4a chrNA:-1--1 NM_146150.2 4 Nrd1 chrNA:-1--1 NM_134065.3 4 Epdr1 chrNA:-1--1 > clustNum = 5 > filteredClust = testData[testData$ClustID == clustNum,] > anyis.na(filteredClust$Genes.Symbol)) [1] FALSE > selectedEntrezIds <- unlist(mget(filteredClust$Genes.Symbol,org.Mm.egSYMBOL2EG)) Error in unlist(mget(filteredClust$Genes.Symbol, org.Mm.egSYMBOL2EG)) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs Another approach fails too: > selectedEntrezIds = select(org.Mm.eg.db,filteredClust$Genes.Symbol, "ENTREZID") Error in .select(x, keys, columns, keytype = extraArgs[["kt"]], jointype = jointype) : 'keys' must be a character vector I am not sure why I am getting this error as the master file from which gene symbols were extracted for testData gives no problem while converting to EntrezID. Would apprecite help on this. Thanks AK

On 08/14/2014 07:58 PM, Atul Kakrana wrote: > Hi All, > > I am getting a strange error converting Gene Symbols to Entrez ID. Here is my code: > > >testData = read.delim("IL_CellVar.txt",head=T,row.names = 2) > > testData[1:5,1:3] > ClustID Genes.Symbol ChrLoc > NM_001034168.1 4 Ank2 chrNA:-1--1 > NM_013795.4 4 Atp5l chrNA:-1--1 > NM_018770 4 Igsf4a chrNA:-1--1 > NM_146150.2 4 Nrd1 chrNA:-1--1 > NM_134065.3 4 Epdr1 chrNA:-1--1 > > > clustNum = 5 > > filteredClust = testData[testData$ClustID == clustNum,] > > anyis.na(filteredClust$Genes.Symbol)) > > [1] FALSE > > > > selectedEntrezIds <- unlist(mget(filteredClust$Genes.Symbol,org.Mm.egSYMBOL2EG)) > Error in unlist(mget(filteredClust$Genes.Symbol, org.Mm.egSYMBOL2EG)) : > error in evaluating the argument 'x' in selecting a method for function > 'unlist': Error in .checkKeysAreWellFormed(keys) : > keys must be supplied in a character vector with no NAs > > Another approach fails too: > > > selectedEntrezIds = select(org.Mm.eg.db,filteredClust$Genes.Symbol, "ENTREZID") > Error in .select(x, keys, columns, keytype = extraArgs[["kt"]], jointype = > jointype) : > 'keys' must be a character vector > > I am not sure why I am getting this error as the master file from which gene > symbols were extracted for testData gives no problem while converting to > EntrezID. Would apprecite help on this. likely your vector of symbols is a factor rather than character (see the "stringsAsFactors" argument on the help page ?read.delim) > select(org.Mm.eg.db, "Ank2", "ENTREZID", "SYMBOL") SYMBOL ENTREZID 1 Ank2 109676 > select(org.Mm.eg.db, factor("Ank2"), "ENTREZID", "SYMBOL") Error in .testForValidKeys(x, keys, keytype) : 'keys' must be a character vector > > Thanks > > AK > > _______________________________________________ > 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 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793