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

[Marc Carlson]

Hi Sugan,

I am having a little bit of Deja Vu.  I feel exactly like I just 
answered this very same question yesterday...  ;)  Here is the link to 
my previous reply.  If you have further questions please feel free to ask.

https://stat.ethz.ch/pipermail/bioconductor/2012-November/049077.html



   Marc





On 11/06/2012 11:44 PM, sugan [guest] wrote:
> 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.
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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