[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


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