[BioC] annotationTools

[David Lyon]

ignore this question I got it working the affy annot format has the dreaded #comments which needs to be taken care of before it would work

Thanks




----- Original Message ----
From: David Lyon <david_lyon3 at yahoo.com>
To: bioconductor at stat.math.ethz.ch
Sent: Thu, June 10, 2010 8:41:48 PM
Subject: [BioC] annotationTools

Does anyone know what this error means and exactly how to fix it?

Thanks a million....

> annotHuman <- read.csv("HG-U133A_2.na30.annot.csv",  colClasses = "character")
>  annotMouse <- read.csv("HT_MG-430A.na30.annot.csv", colClasses = "character")
> homologene<-read.delim('homologene.data',header=FALSE)
>  target_species <- 10090
> mappingTable <- ps2ps(annotHuman,annotMouse,homologene,target_species)
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'



ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
http://media.affymetrix.com/analysis/downloads/na30/ivt/HG-U133A_2.na30.annot.csv.zip
http://media.affymetrix.com/analysis/downloads/na30/ivt/HT_MG-430A.na30.annot.csv.zip

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