[BioC] limma toptable missing ProbeId/ documentation question

[James W. MacDonald]

Hi Björn,

Ignore my last email - I don't even have R-2.2.X on my computer anymore, 
so I got the most recent version for R-2.3.0.

Anyway, the problem here is that you are calling toptable() instead of 
topTable(). The latter will correctly extract the genelist from your fit 
object.

Best,

Jim



Björn Usadel wrote:
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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