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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor