Entering edit mode
Mayte Suarez-Farinas
▴
300
@mayte-suarez-farinas-694
Last seen 10.3 years ago
Dear Collegues:
I built an annotation package (using AnnBuilder) to work with
mu11KsubA
and B Chips. See below the script:
----------------------------------------------------------------------
--
library(AnnBuilder)
myDir<-tempdir()
Ann1<-read.table(file='/home/MyAnn/affy_Mu11KA',skip=1,header=TRUE,as.
is=TRUE,sep='\t',quote='',comment.char="")
Ann2<-read.table(file='/home/MyAnn/affy_Mu11KB',skip=1,header=TRUE,as.
is=TRUE,sep='\t',quote='',comment.char="")
Ann<-rbind(Ann1[,c("Probe.ID","UniGene.ID")],Ann2[,c("Probe.ID","UniGe
ne.ID")])
write.table(as.matrix(Ann), file = file.path(myDir, "AnnDan"),sep =
"\t", row.names = FALSE, col.names = FALSE, quote=FALSE)
ABPkgBuilder(baseName=file.path(myDir, "AnnDan"),
srcUrls=getSrcUrl("ALL",organism='mouse'), baseMapType = 'ug',otherSrc
=
NULL, pkgName="mu11KABannot", pkgPath=myDir, organism =
"mouse",version = "1.3.0", makeXML = TRUE,
author = list(author = "MSF",maintainer =
"mayte@babel.rockefeller.edu"), fromWeb = TRUE)
------------------------------------------------
Then I install the package (using R CMD INSTAll.... ) and It was Ok.
But with some list of genes it fails. See example below using all the
genes in Chips A B.
anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler())
Error in get(x, envir, mode, inherits) : variable "GO:0050983" was not
found
> aaf.handler()
[1] "Probe" "Symbol" "Description"
[4] "Function" "Chromosome" "Chromosome Location"
[7] "GenBank" "LocusLink" "Cytoband"
[10] "UniGene" "PubMed" "Gene Ontology"
[13] "Pathway"
It works OK when you eliminate the GO column:
> anntable<-aafTableAnn(probesids,chip=AnnPkg,aaf.handler()[-12])
Did I make a mistake in the building procedure or it is something
related with the internal extructure of GO package??