[BioC] ExpressionSet or MAList

Gordon K Smyth smyth at wehi.EDU.AU
Tue May 6 09:32:29 CEST 2008

Dear Dan,

It does rather depend on the microarray platform you're using.  If you're 
generating single channel data, such as from Affymetrix or Illumina 
arrays, you certainly shouldn't be using MAList.  On the other hand, if 
your data is two-colour, I wouldn't myself find ExpressionSet satisfactory 
because it doesn't "know" anything about the structure of two-colour data. 
Rather than ExpressionSet itself, the real alternative to MAList would be 
a data class inheriting from ExpressionSet with two-colour features added. 
There may be such a class already on Bioconductor, but I'm not familiar 
with any.

Best wishes

> Date: Wed, 30 Apr 2008 17:26:15 +0100
> From: Daniel Brewer <daniel.brewer at icr.ac.uk>
> Subject: [BioC] ExpressionSet or MAList
> To: bioconductor at stat.math.ethz.ch
> 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.
> To my mind MAList stores the annotation with the dataset which I feel is
> an advantage whereas ExpressionSet is the base implementation for many
> libraries.
> Dan
> -- 
> **************************************************************
> Daniel Brewer, Ph.D.
> Institute of Cancer Research
> Email: daniel.brewer at icr.ac.uk
> **************************************************************

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