[BioC] Annotation Tools package

[Alexandre Kuhn]

Hi Giu,
Affymetrix has added comment lines in their annotation files (starting with
'#'). Skip these when reading the files and use

>
annotHuman<-read.csv('HG-U133_Plus_2.na27.annot.csv',colClasses='character',
comment.char='#')
>
annotMouse<-read.csv('Mouse430A_2.na27.annot.csv',colClasses='character',com
ment.char='#)

instead of the commands shown in the help/vignette. I will update
help/vignette accordingly.

Also, the function ps2ps only uses information from Affymetrix and
HomoloGene files so that you do not need to load chip packages from
Bioconductor (mouse430a2.db and hgu133plus2.db).

Alexandre


-----Message d'origine-----
De : bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] De la part de Giusy Della
Gatta
Envoyé : dimanche 21 juin 2009 22:06
À : bioconductor at stat.math.ethz.ch
Objet : [BioC] Annotation Tools package

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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