[BioC] samr and Spike in

James W. MacDonald jmacdon at med.umich.edu
Tue Jan 31 20:30:18 CET 2006

Mohammad Esad-Djou wrote:
> Hello, 
> I would like to use samr for spike in genes (HG-U13A). I get expression values through affy Package and MAS 5.0.
>>raw <- ReadAffy(...)
>>exprs <- expresso(..)
>>mat <- exprs(exprs)
> and separate Spike in genes from expression values:
>>G1 <- mat[c(spike in genes),1:14] 
>>G2 <- mat[c(spike in genes),15:28] 
> and produce a list:
>>data=list(x=G1,y=G2, geneid=as.character(1:nrow(G1)),genenames=paste("g",as.character(1:nrow(G1)),sep=""), logged2=TRUE)

You might take a look at the man page for samr:


     data: Data object with components x- p by n matrix of features, one
           observation per column (missing values allowed); y- n-vector
           of outcome measurements; censoring.status- n-vector of
           censoring censoring.status (1= died or event occurred,
           0=survived, or event was censored), needed for a censored
           survival outcome

The data object is supposed to have x = p x n matrix of your expression 
values and y = an n-vector of outcome measurements.

You are passing two matrices instead of a matrix and a vector.

If I were trying to do something like this, I would use the siggenes 
package instead of samr. Holger Schwender has put a lot of work into 
making siggenes user-friendly so you probably have a better chance of 
getting things to work out.



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

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