[BioC] rownames in topTable and posterior probability

[Adaikalavan Ramasamy]

Thank you Dr. Symth (and Dr. MacDonald).

As you have correctly suspected, the problem is with the input
'onebatch' which is a matrix. The matrix was actually extracted from the
exprSet during an intermediate step, stored and used for subsequent
analysis here.

Is it a sensible suggestion for the lmFit() to set the rownames of the
matrix as the gene names _if_ the class of object was matrix ? Might try
later today to fudge to include a branch for is(object, "matrix") in the
existing lmFit() code and post it. But is this worth the effort ?

I presume there might be a few people who prefer to work with matrix of
gene expression. E.g. those who only get the finalised dataset as the
output of some public repositories. Or is it easier to convert a matrix
to an exprSet and work from there ?

Thank you.

Regards, Adai



On Sun, 2005-02-27 at 00:11 +1100, Gordon K Smyth wrote:
> > Date: Fri, 25 Feb 2005 11:33:57 +0000
> > From: Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
> > Subject: [BioC] rownames in topTable and posterior probability
> > To: BioConductor mailing list <bioconductor at stat.math.ethz.ch>
> >
> > topTable() in limma packages returns the row numbers and it would be
> > useful to see the row names (i.e. Affy ID) instead.
> 
> topTable() already does this, as can be seen from the case studies in the User's Guide.  For
> example, the Ecoli and Estrogen case studies show top tables with Affy IDs included automatically.
> 
> > I am aware that I
> > may supply the 'genelist' argument but help("topTable") says :
> >
> > 	genelist: data frame or character vector containing gene
> > 	 	  information. If not specified, this will be taken
> > 		  from the 'genes' component of 'fit'.
> 
> This is not normally required.  Have you not looked at the examples in the User's Guide?
> 
> > My usual usage is as follows
> >
> > fit  <- lmFit(onebatch, design)
> > fit2 <- contrasts.fit( fit, cont.m )
> > fit2 <- eBayes(fit2)
> >
> > topTable(fit2)
> >                M         t      P.Value         B
> > 12358 -0.8636721 -7.585040 3.808592e-05 11.958486
> > 48048 -0.8765769 -7.400093 7.417187e-05 11.363358
> > ...
> >
> > But I found no genes component in fit via fit$genes or str(fit). Same
> > goes for fit2. I doing something wrong ?
> 
> You haven't told use what sort of object 'onebatch' is.  If onebatch is an object from which gene
> names can be extracted, e.g., an exprSet, then they should be included in 'fit'.  If 'onebatch'
> doesn't include gene names, you can't really expect them to be in fit.
> 
> Gordon
> 
> > Thank you.
> >
> > Regards, Adai
> 
> 
>