[Bioc-devel] Subsetting affybatch and exprset objects

[Rafael A. Irizarry]

the problem is th if you subset eset by the first dimension then you 
loose the position structure, and as a consequence the locations of pms
and mms held in the cdfenv are no longer meaningful. if there are any 
suggestions on what eset[i,] should return id be happy to consider them.

On Tue, 13 Apr 2004, Crispin Miller wrote:

> Hi,
> Apologies if I should have sent this to the main bioconductor list...
> and tell me if you'd have preferred it there! ;-)
> 
> I've noticed an issue with subsetting ExprSet and AffyBatch objects -
> and wondered what what peoples' thoughts were:
> If I do a subsetting operation of an exprSet with 6 chips in, I get
> this:
> 
> > eset.mas[1,]
> Expression Set (exprSet) with 
> 
>    1 genes
>    6 samples
> 
> > eset.mas[,1]
> ...
>    22283 genes
>   1 samples
> 
> 
> However, if I do the same with AffyBatch I get this:
> 
> > eset[1,]
> AffyBatch object
> ...
> Number of samples=1
> Number of genes=22283
> 
> >eset[,1]
> AffyBatch object
> Number of samples=6
> Number of genes=22283
> 
> 
> Soooo, to subset and exprSet by chip I have to type eset[,x], but for an
> AffyBatch I must type: eset[x,], which is particularly confusing since
> AffyBatch is a subtype of exprSet... Would it be possible/a good idea,
> to make these two incantations the same for both classes?
> 
> Crispin
>  
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