[BioC] ExpressionSet or MAList

[Martin Morgan]

Hi Daniel --

Daniel Brewer <daniel.brewer at icr.ac.uk> writes:

> Hi,
>
> I am starting to think about grouping a series of microarray datasets
> into bioconductor objects so that I can quickly look to see how a gene
> behaves in each dataset.  The two main options seem to be to use
> ExpressionSet or Limma's MAList.  Has anyone got an opinion on which
> would be best to use or the advantages and disadvantages of both.

Some biases on my part, but...

I guess either ExpressionSet or MAList is really meant to represent a
single 'experiment'. Sounds like you're going to create a collection
of experiments, so a collection of ExpressionSet or MAList objects (it
would be a mistake, I think, to jam all your experiments into a single
object of either of these classes).

> To my mind MAList stores the annotation with the dataset which I feel is

Storing annotations with the object can be a bad thing if the
annotations are the same, because then there are effectively different
variants of the same annotation, one for each object. These will
inevitably drift apart, leading to confusion. There is also a memory
use issue.

That said, annotations can be added to ExpressionSet, specifically
using featureData to store an AnnotatedDataFrame (data.frame +
annotation on column labels).

> an advantage whereas ExpressionSet is the base implementation for many
> libraries.

ExpressionSet is a little more tightly designed than MAList (MAList is
essentially a list and so can contain (or not contain) any data;
ExpressionSet is an S4 class that has to contain certain data. While
you lose on freedom with ExpressionSet, the constriction probably
comes with a benefit in terms of greater certainty about what the
object actually contains. This imposed uniformity likely has benefits
when the number of experiments you're managing increases. Many users
probably view their MAList / ExpressionSet as 'read-only', so for
these users the fact that you could do something to mess up an MAList
really is only an academic possibility (you can also do things to mess
up an ExpressionSet, again maybe just a bit harder to do that).

ExpressionSet also contains an experimentData slot, which would be an
ideal location to document which experiment the ExpressionSet
represents.

> Dan

hope that helps,

Martin

> -- 
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> Daniel Brewer, Ph.D.
> Institute of Cancer Research
> Email: daniel.brewer at icr.ac.uk
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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