[BioC] Multtest

[James MacDonald]

You are making things difficult on yourself. All multtest wants is a
matrix of data and a classlabel vector. The .RData file you use in the
vignette is simply to make things easier to distribute.

Do something like this:

eset <- rma(Data) #Exactly equal to what you did, but I think it will
be much faster
teststat <- mt.teststat(exprs(eset), treat) # Here I am assuming that
treat is a  vector of 0's and 1's

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Roger Vallejo" <rvallejo at psu.edu> 03/08/04 09:30AM >>>
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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