[BioC] SAM in siggenes package

[Anna Cao]

Hi,

I'm trying to run SAM using the siggenes package in R (version 1.8.1 in
Window XP). I have a 16247x204 matrix containing all the arrays in my
experiment. This matrix includes several experimental conditions including
replicates. I need to run sam for each experimental condition. I try the
following command and got this error. 

sam(RG.alls, x=RG.alls$R[1:16], y=RG.alls$G[1:16])
Error in as.double.default(structure(list(structure(c(NA, NA, NA, NA,  : 
        (list) object cannot be coerced to double

I assume this error may be related to all the blank (NA) points I have in
the matrix. Are there any ways to remove these empty spots for each set of
replicates without having to export and arrange the matrix elsewhere?

Anna