[BioC] Annotation Tools package
Giusy Della Gatta
gd2253 at columbia.edu
Mon Jun 22 04:06:18 CEST 2009
Hi everybody,
I need to convert my mouse affymetrix ID into their correspondent human orthologues ID
(more precisely I have to go from mouse430a2 to HG133_Plus2).
I found this package inBioC: AnnotationTools.
First of all, I am trying to recover the orthologues annotations from mouse
to human array by following the commands from the tutorial, but I have an error:
> library(annotationTools)
>library(mouse430a2.db)
> library(hgu133plus2.db)
> annotHuman<-read.csv('HG-U133_Plus_2.na27.annot.csv',colClasses='character')
> annotMouse<-read.csv('Mouse430A_2.na27.annot.csv',colClasses='character')
> homologene<-read.delim('homologene.data',header=FALSE)
> targetSpecies <- 10090
> orthoTable <- ps2ps(annotHuman, annotMouse,homologene, 10090)
Getting source gene IDs...
Getting orthologous genes...
Getting orthologous probe sets...
Error in sum(l) : invalid 'type' (list) of argument
In addition: Warning messages:
1: In is.na(geneid) :
is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(geneid) :
is.na() applied to non-(list or vector) of type 'NULL'
Does anyone of us tell me something about this error?
Thank you in advance!
Giu
More information about the Bioconductor
mailing list