[BioC] Annotation using org.At.tair.db package in R

[sugan [guest]]

Iam using R version 2.15 in a linux operating system. I have a matrix consisting of the  gene ids and their specific signal intensity values as follows( a subset of the whole matrix) :

     probes GSM362180    GSM362181  GSM362188    GSM362189  GSM362192
     244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647
     244902 5.194528083 4.985930299 4.817426064 5.151654407 4.838741605
     244903 5.412329253 5.352970877 5.06250609  5.305709079 8.365082403
     244904 5.529220594 5.28134657  5.467445095 5.62968933  5.458388909
     244905 5.024052699 4.714631878 4.792865831 4.843975286 4.657188246
     244906 5.786557533 5.242403911 5.060605782 5.458148567 5.890061836

I would like to extract only the first column as follows :
ids <- scr[,2]
and then I got a factor[2368]

 And tehn I proceeded to the annotation as follows:

     biocLite("GO.db")
     library("AnnotationDbi")
     biocLite("org.At.tair.db")
     biocLite("ath1121501.db").
     genenames <-  org.At.tairGENENAME[ids] #map the probe ids to the gene names in TAIR

     The output of which is  AnnDbBiMap[1]

     number<-org.At.tairENTREZID[ids] #map the probe ids to the gene ids in TAIR
     The output of which is AnnDbBiMap[1]
    
     And then I try to merge both the lists as : 
     xx<-toTable(entrez)
     yy<-toTable(number)
     complete<-merge(xx,yy)

I get an error in this step and unable to proceed further.The error reads:
         Error in fix.by(by.y.y): 'by' must specify uniquely valid column(s) 

Is it because ids <- scr[,1] is a factor ?


 -- output of sessionInfo(): 

R version 2.15
Linux.

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