This is probably a really astute group to ask this question of:- -
when did
da dchip.exe download seemingly gone under some Yahoo groups
downloading
scheme?
Thank You,
-mL
951.328.9930 apartment
------------------------------------------------------------------
Matthew Lyon lab (951) 827-4736
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
