[Bioc-devel] Problem Mogene10stprobeset

jarod_v6 at libero.it jarod_v6 at libero.it
Thu Jun 21 15:33:54 CEST 2012


Hi there!!!
 I'm a student and I want to learn how to use bioconductor but I have this 
problem  
I use this script for  analysis the data  starting from .CEL data. After I 
prepare  annotated gene I found annotate only 91 gene... I don't Understand why 
happed that.
Someone Can Help Me?

source("http://www.bioconductor.org/biocLite.R")
biocLite("affy")
biocLite("limma")
biocLite("annotate")
biocLite("mogene10stprobeset.db")
install.packages("R2HTML")


library(affy)
library(limma)
library(annotate)
library("mogene10stprobeset.db")
library(R2HTML)

data<-ReadAffy()
eset <- rma(data)
class(eset)
eset at annotation

# Get the transcript cluster IDs from the expressionset
ID <- featureNames(eset)
Symbol <- getSYMBOL(ID, "mogene10stprobeset.db")
Name <- as.character(lookUp(ID, "mogene10stprobeset.db", "GENENAME"))
Ensembl <- as.character(lookUp(ID, "mogene10stprobeset.db", "ENSEMBL"))
luisa<-exprs(eset) 
martina<-data.frame(ID=ID,Symbol=Symbol, Name=Name, Ensembl=Ensembl,
geee=luisa, stringsAsFactors=F)
martina[martina=="NA"] <- NA
write.table(martina,"DAti_an.csv",sep="\t")


It is annotatet only the last 91 ID....Why?

Thanks in advance for any Help
M.



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