[BioC] limma toptable missing ProbeId/ documentation question

[Björn Usadel]

Dear List,

Sorry for posting a very minor thing or if this has been posted already,

using limma 2.2.13
I don't get ProbeIDs back when  calling toptable

toptable(fit,num=1)
             M        t      P.Value    adj.P.Val        B
22488 13.32117 197.5873 1.039258e-15 7.791015e-13 23.66308

It does work though when calling
toptable(fit,num=1,genelist=fit$genes)
             ID        M        t      P.Value    adj.P.Val        B
22488 267388_at 13.32117 197.5873 1.039258e-15 7.791015e-13 23.66308

This is no problem whatsoever, but help toptable states

"genelist: data frame or character vector containing gene information.
          If not specified, this will be taken from the 'genes'
          component of 'fit'."
(I hope my docu is also up to date as well)

and genelist is set to NULL by default.
Furthermore nowhere in toptable is fit$genes referenced (at least I 
coudln't find it)

a possible fix  which works for me with my limited datasets but I have 
no clue about the internals of the fit object:

if (is.null(genelist))
    +++genelist<-fit$genes
        ---tab <- data.frame(M = M[top])
    ---else {
        if (is.null(dim(genelist)))
            tab <- data.frame(ProbeID = I(genelist[top]), M = M[top])
        else tab <- data.frame(genelist[top, , drop = FALSE],
            M = M[top])
    ---}

alternatively one could just change the docu of toptable.

This is really only an extremly minor thing, but might possibly lead to 
confusion.


Kind regards,

Björn