[BioC] GO annotation in R

[priya [guest]]

I have the matrix as follows :

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[,1]
and then

biocLite("GO.db")
library("AnnotationDbi")
biocLite("org.At.tair.db")
biocLite("ath1121501.db")
library("ath1121501.db")
genenames <-  org.At.tairGENENAME[ids]
number<-org.At.tairENTREZID[ids]
xx<-toTable(entrez)
yy<-toTable(number)
complete<-merge(xx,yy)

I get an error in this step and unable to proceed further. Is it because ids <- scr[,1] is a factor ?

Iam not sure how to store the id names to carry out the annotation correctly .I would like to use GO.db to find the Terms associated with the go Ids, displaying the result as a data frame with my probes and their corresponding TAIR ID and TAIR genename and annotation.


 -- output of sessionInfo(): 

R version 2.15
Linux.

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