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

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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor