[BioC] SAM in siggenes package

[Sean Davis]

On 12/19/03 13:50, "Anna Cao" <yunie at caltech.edu> wrote:

> 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

Anna,


Actually, assuming that you are doing a one-class evaluation (as it looks
like you are interested in finding genes disregulated in the first 16
columns), I think that your call should look like:

sam(RG.alls, x=c(1:16),y=NULL)

If you have NAs, see the parameter na.rm from ?sam to see what sam does when
NAs are present. 

Sean