[BioC] Error while mapping SYMBOLS to ENTREZID

Atul Kakrana atulkakrana at outlook.com
Fri Aug 15 04:58:16 CEST 2014

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$ClustID == clustNum,]
 > any(is.na(filteredClust$Genes.Symbol))


 > selectedEntrezIds <- 
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, 
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.



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