Hi,

 

We are using samr package in R version 1.25 to run SAM algorithm. To execute
SAM algorithm, we used following functions in R. 

 

.         To run SAM algorithm we used following commands/functions 

 

        set.seed(100)

        x<-matrix(rnorm(1000*20),ncol=20)

        dd<-sample(1:1000,size=100)

 

        u<-matrix(2*rnorm(100),ncol=10,nrow=100)

        x[dd,11:20]<-x[dd,11:20]+u

 

        y<-c(rep(1,10),rep(2,10))

 

        data=list(x=x,y=y,
geneid=as.character(1:nrow(x)),genenames=paste("g",as.character(1:nrow(x)),s
ep=""), logged2=TRUE)

        samr.obj<-samr(data, resp.type="Two class unpaired", nperms=100)

                                

                   Algorithm was successfully executed using above commands.

 

.         After executing above function we tried plotting graph for the
algorithm using following two statements:

 

        samr.assess.samplesize.obj<- samr.assess.samplesize(samr.obj, data,
log2(1.5))
 
        samr.assess.samplesize.plot(samr.assess.samplesize.obj)

 

Graph was plotted successfully with X-axis showing Expected Score and Y-axis
showing Observed score.

 

.         To retrieve Observed score for above graph, we ran following
command on R which returned us Observed score for each input gene
successfully:

 
        delta.table<-samr.compute.delta.table(samr.obj)
        del<- 0.3
        siggenes.table<- samr.compute.siggenes.table(samr.obj, del, data,
delta.table, min.foldchange=0, all.genes=TRUE) 
 
 
We also want Expected score values plotted in the Graph. Please let us know
using which function we can retrieve Expected score values for. 
 
Any help on the same would be appreciated.

 

Thank you,

Jaydeep


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