[Bioc-devel] MIAPE/MIAME in eSet

Vincent Carey 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

> getClass("MIAME")
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

Name:  .__classVersion__
Class:          Versions

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.
> Best,
> Florian P Breitwieser
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