[BioC] (no subject)

[Seth Falcon]

On 15 Nov 2005, khan at cshl.edu wrote:

> Dear List,
> I am using siggenes1.2.17 on R 2.1.1. I have an object of class
> "sumSAM". I want to obtain a list of differentially expressed genes,
> so I try the following:
> sum.sam.out<-summary(sam.out,3.0,ll=FALSE)
> When I try to get the list of significant genes
> sum.sam.out$row.sig.genes
> I get a NULL. 
> I checked the slotNames(sum.sam.out)
> "row.sig.genes" "mat.fdr" "mat.sig" "list.args"
> but they are all NULL.  

How did you check?  If sumSAM is an S4 class (which seems to be the
case if slotNames gives useful info), then you want to access the
contents of the slots using "@" or slot().  For example,

sum.sam.out at row.sig.genes

HTH,

+ seth