[Bioc-devel] Problem Mogene10stprobeset

[James W. MacDonald]

On 6/21/2012 9:33 AM, jarod_v6 at libero.it wrote:
> 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")

Since you are using the affy package to process these data, you are 
summarizing at the transcript level rather than the probeset level. So 
you want the mogene10sttranscriptcluster.db package.

Best,

Jim


> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099