[BioC] outliers removal

[Roger Vallejo]

Bioconductor Fellows,

I have 8 samples (affy arrays with 22,690 probesets). I would like to:

1.   Remove outliers and select some genes (using raw signal data from
*.CEL files), to then

2.   Run the standard data processing technique (let say just RMA)

 

Obviously I have problems on doing these. I have used these R commands:

 

*******************Begin R commands**********************

Data <- ReadAffy()

exprmatf=exprs(Data)

dim(exprmatf)

 

# Floor & ceiling of raw data

exprmatf [exprmatf <10] <-10 

exprmatf [exprmatf >25000]<-25000

 

# Preliminary selection of genes

tmp1<-apply(exprmatf,1,max)

tmp2<-apply(exprmatf,1,min)

which1<-(1:506944)[(tmp1/tmp2)>2]

which2<-(1:506944)[(tmp1-tmp2)>100]

exprmatf.sub <-intersect(which1,which2)

exprmatfilt  <-exprmatf[exprmatf.sub,]

 

Dataf<- write.table(exprmatfilt)

library(vsn)

normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")

esetf <- expresso(Dataf, bg.correct=FALSE, normalize.method="vsn",
pmcorrect.method="pmonly", summary.method="medianpolish")

 

*******************End R commands**********************

 

The last command does not run! 

I got this error message:

 

normalization: vsn 

PM/MM correction : pmonly 

expression values: medianpolish 

normalizing...Error in normalize(afbatch, normalize.method) : 

        No direct or inherited method for function "normalize" for this
call

 

I would appreciate somebody indicating why is that? Or what I am doing
wrong.

Thank you very much for the help!!

 

Roger

 

 

 

Roger L. Vallejo, Ph.D.

Assist. Professor of Genomics & Bioinformatics

Genomics & Bioinformatics Laboratory

Department of Dairy & Animal Science

The Pennsylvania State University

305 Henning Building

University Park, PA 16802

Phone:       (814) 865-1846 

Email:        rvallejo at psu.edu

 


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