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

[stace]

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 then 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 ? How would it be possible to
extract it as :

ids<- c("244901", "244902", "244903",......) 

I cannot do the above manually because its a large matrix.


 -- output of sessionInfo():

R version 2.15
Linux.



--
View this message in context: http://r.789695.n4.nabble.com/Annotation-using-org-At-tair-db-package-in-R-tp4648711.html
Sent from the R help mailing list archive at Nabble.com.