
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)

> samr.obj<-samr(data, resp.type="Two class paired", nperms=100)
Error in check.format(y, resp.type = resp.type, censoring.status = censoring.status) :
 Error in input response data: response type Two class paired specified; values must be -1, 1, -2, 2, etc
>

what isn't correct? And how can I write correctly?

Thanks,

Mohammad Esad-Djou

 

 







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