[Bioc-devel] MIAPE/MIAME in eSet
stvjc at channing.harvard.edu
Wed Oct 13 13:04:15 CEST 2010
I don't know of any plans to generalize this, but I would tend to
agree that eSet should not commit one to a microarray-oriented
experiment metadata element. I looked briefly at the PSI resources
and see that schemata have been generated for various assay types. So
it's not the case that there's a simple way of comparing the PSI
schema to what is already
present in MIAME.
Currently we have
Class "MIAME" [package "Biobase"]
Name: name lab contact title
Class: character character character character
Name: abstract url pubMedIds samples
Class: character character character list
Name: hybridizations normControls preprocessing other
Class: list list list list
Extends: "Versioned", "characterORMIAME"
All but "hybridizations" would seem potentially relevant to any
high-throughput experimental paradigm. So except for some naming
inelegance, I would propose that MIAPE class design proceed by
extending MIAME. Your eSet extensions can load the experimentData
slot with MIAPE-CC, -MS and so forth, as you like
(http://www.psidev.info/index.php?q=node/91), but we would leave the
class of experimentData as MIAME to avoid ramifications of changing a
central class definition.
This is my humble opinion only, and more discussion is clearly
warranted. I would conclude by saying that IMHO changing the eSet
definition is not to be taken lightly, and functional benefits of such
a change need to be very substantial to warrant this.
On Wed, Oct 13, 2010 at 6:03 AM, Florian P. Breitwieser
<fbreitwieser at cemm.oeaw.ac.at> wrote:
> Dear developers,
> we are developing a package for Bioconductor, using eSet as a container for
> the assay data.
> It is Mass spectrometry proteomics data. In the same manner as MIAME exists
> for Microarrays, there is a minimum information about a proteomics
> experiment (MIAPE) defined by the Proteomics Standards initiative.
> Currently, experimentData slot in eSet is of class MIAME. Are there plans to
> generalize this?
> I am happy to help, and to contribute a MIAPE class definition.
> Florian P Breitwieser
> Bioc-devel at stat.math.ethz.ch mailing list
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