[BioC] Multtest

[Roger Vallejo]

I would like to have an idea on my FDR and I thought that the MULTTEST
package will do it.

I read the MULTTEST.pdf manual and it is quite clear how to run the
golub.RData example file.   The problem is on how to run MULTTEST in my
arrays data. 

To begin, how do I make the *.RData file using my data? Which of my
files do I use? 

It seems that I have to use the output file after using this R function:

> eset <- expresso(Data,bgcorrect.method="rma",
normalize.method="quantiles", pmcorrect.method="pmonly",
summary.method="medianpolish")

I used then:

> roger=exprs(eset)


> roger.gnames=geneNames(eset)

> roger.cl=treat


 

> data(roger)

> dim(roger)

> roger[1:4, 1:4]

> dim(roger.gnames)

> roger.gnames[1:4, ]

> roger.cl

 

I got error messages. I opened the golub.RData file and it looks
completely different to my "eset" or "roger" file. So this is the reason
for the errors on running MULTTEST .

I would appreciate instructions how do I make the *.RData file to run
the multtest package.

Many thanks in advance for the help.

Roger

             

 

Roger L. Vallejo, Ph.D.

Assist. Professor of Genomics & Bioinformatics

The Pennsylvania State University

Department of Dairy & Animal Science

305 Henning Building

University Park, PA 16802

Phone:  (814) 865-1846 

Fax: (814) 863-6042

Email:   rvallejo at psu.edu <mailto:rvallejo at psu.edu> 

 


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