[Bioc-devel] Subsetting affybatch and exprset objects

Crispin Miller CMiller at PICR.man.ac.uk
Tue Apr 13 13:44:48 CEST 2004

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

> 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

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?


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