Annotation Tools package
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@giusy-della-gatta-3518
Last seen 7.1 years ago
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='charac ter') > 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
GO mouse430a2 probe convert annotationTools GO mouse430a2 probe convert annotationTools • 772 views
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@alexandre-kuhn-3522
Last seen 7.1 years ago
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='characte r',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 Envoy??: dimanche 21 juin 2009 22:06 ??: 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='charac ter') > 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 _______________________________________________ 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
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