[BioC] calling SAM using siggenes package

[saran.2.vardhanabhuti at gsk.com]

Hi,
        I have a question about using sam method in siggenes package. My R 
version is 1.9.0 and my siggenes package version is 1.0.6.
        I took a look at the usage page for sam and I'm a little confused 
about two arguments: data and cl since it is not really clear to me what 
their format should be.
        I have a file testdata.txt that contains 6 columns and each row 
contains intensity value. This data represent unpaired two class 
comparisons, each class has 3 replicates hence there are 6 columns.
        So in R I do scan data as follow:
        > data<-scan("testdata.txt")
        Then for cl argument, it is a vector containing the class labels 
of the samples. In this case I set the cl as follows:
        > cl<-c(0,0,0,1,1,1)
        This is to show that I have two classes for comparisons. Am I 
doing this wrong? Since I don't seem to find anything on this format on 
the internet at all.

        So I went ahead and execute sam as follows:
        > samdata<-sam(data,cl)

        Then I got the following error:
        Error in data[, c(x,y)] : incorrect number of dimensions.

        Any advice on this will be greatly appreciated.

Thank you,
Saran
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