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Guido Hooiveld
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@guido-hooiveld-2020
Last seen 6 days ago
Wageningen University, Wageningen, the …
I face a small issue, which likely is easy to solve.....:
I would like to automatically retrieve annotation information for expressionSets, but somehow I don't get it to work...:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"character"’
Any suggestions to solve this?
Thanks,
Guido
> library(affyPLM) > affy.data <- ReadAffy() > > x.norm <- rma(affy.data) Background correcting Normalizing Calculating Expression > > head(featureNames(x.norm)) [1] "1415670_at" "1415671_at" "1415672_at" "1415673_at" "1415674_a_at" [6] "1415675_at" > > annotation(x.norm) [1] "mouse4302" > > require(paste(annotation(x.norm),".db", sep=""), character.only=TRUE) Loading required package: mouse4302.db Loading required package: org.Mm.eg.db > > paste(annotation(x.norm),".db", sep="") [1] "mouse4302.db" > > anno.result <- select(paste(annotation(x.norm),".db", sep=""), + keys=featureNames(x.norm), columns=c("ENTREZID","SYMBOL"), keytype="PROBEID") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"character"’ >
Thanks Martin, working nicely now with
get
!