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.
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