[BioC] samr and Spike in

[James W. MacDonald]

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:

Arguments:

     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.

Best,

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