[BioC] AveExp" column has dissappeared from limma topTable

[Mikhail, Amy]

Hi Gordon,

Thanks for your reply, just tried subsetting without exprs() and it
returned a sub-setted exprSet, as you said... So just wondering, when
does one actually need to use exprs() and when can I get away without
it?

Also, what is the difference between an exprSet and an ExpressionSet?

Many thanks,

Amy

-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Tuesday, April 03, 2007 10:56 PM
To: Mikhail, Amy
Cc: bioconductor at stat.math.ethz.ch
Subject: AveExp" column has dissappeared from limma topTable

> Date: Mon, 2 Apr 2007 14:23:45 +0100
> From: "Mikhail, Amy" <a.mikhail at abdn.ac.uk>
> Subject: Re: [BioC] "AveExp" column has dissappeared from limma
> 	topTable
> To: "Marcus Davy" <mdavy at hortresearch.co.nz>
> Cc: bioconductor at stat.math.ethz.ch
>
> Hi Marcus,
>
> "Mosquito" is a subset of my original exprSet (with some probesets 
> taken out).  So it is just a matrix

There is no reason why a subset of an exprSet should not be an exprSet
also.  Just subset the object without using exprs().

Best wishes
Gordon

> and now that I look, there is no "Amean"
> element in my fit object.  I didn't know that Amean would not be 
> derrived for matrices, thanks for pointing that out.
>
> Many thanks,
> Amy