samr and Spike in
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@mohammad-esad-djou-1159
Last seen 10.2 years ago
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Matthew Lyon ▴ 120
@matthew-lyon-1579
Last seen 10.2 years ago
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
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@james-w-macdonald-5106
Last seen 14 hours ago
United States
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
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