[BioC] Begginig doubts about layout and toptable

[Pete]

> Hi everyone.
>
> I use the Imagene out put file.
>
> I analyse it in limma very well, but I have a doubt in layout.
>
> In the limma manual, layout are acquired by the getLayout(GAL) function.
In
> my case, I include layout by "hand", using the list, for exemplo:
> layout=list(ngrd.r=4,...). Have another hand (way) to enter layout in
> layout?
if your raw data was read in to RG then you can use

layout<-RG$printer

>
> Another doubt:
>
> In the limma manual have to type of toptable:
>
> 1. topTable(fit, n=30, adjust="fdr")
>  in this type I have a error.
>
> 2. toptable(number=30,genelist=gal,fit=fit,eb=eb,adjust="fdr")
>  in this case I have a error because I dont have the gal file.
>
> How do I do to fit genelist in my case (imagene out put file).

Again if your data is in RG use

genes<-RG$genes
toptable(number=30, genelist=genes, fit=fit, eb=eb, adjust="fdr")


Hope that helps

Pete Underhill
Microarray Facility
MRC Harwell