[BioC] ExpressionSet or MAList

Daniel Brewer daniel.brewer at icr.ac.uk
Thu May 1 17:39:28 CEST 2008

Martin Morgan wrote:
> 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


I think you have sold me on the idea of ExpressionSet (mainly becuase of
the MIAME stuff in ExperimentData), but I have one question about it.
Is there anyway to store associated detection p-values/weights with it?
 This would be useful information to retain for later analysis.


Daniel Brewer, Ph.D.

Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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