[BioC] limma toptable missing ProbeId/ documentation question
usadel at mpimp-golm.mpg.de
Wed Apr 12 11:55:48 CEST 2006
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
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
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:
---tab <- data.frame(M = M[top])
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
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