[Bioc-devel] RFC: eSet with two color data

Kevin R. Coombes krc at mdacc.tmc.edu
Wed Mar 21 16:13:15 CET 2007


Having thought about this several times, I keep coming back to [A], for 
exactly the reasons you point out. It has the decided advantage of 
generalizing to any number of colors (including 1!) -- which actually 
suggest that ExpressionSet might be modified to include your required 
columns.  One might, however, prefer "Label" instead of "dye" to allow 
for somewhat more generality.


Wolfgang Huber wrote:
> Dear all,
> I hope that this question is not too tedious for those who have already
> thought hard about it, but I am not aware of consensus and good
> documentation in Biobase on this topic:
> How can we best represent preprocessed, normalised data from a set of
> two- (or n-) colour arrays in an eSet like structure? I would like to
> keep the intensity information of each channel, and not reduce to
> M-values since that looses information.
> I see two options:
> A) in an ExpressionSet-derivative called e.g. "ExpressionSetWithColors"
> with ncol = n times the number of arrays, and with mandatory phenoData
> columns named e.g. "arrayID" and "dye" .
> B) in an eSet-derivative with ncol = the number of arrays, and n
> congruent matrices in the assayData slot.
> Currently I prefer A, because
> - most of the infrastructure is already there and the additional work is
> little
> - in B, the interpretation of the phenoData columns gets mushy because
> some columns will refer to the arrays, others to one particular sample
> of the n hybrised to each array, and we need additional infrastructure
> to resolve that.
> Is there anything that someone can point out that I am not aware of?
> Also (different topic:) do we already have an ontology in place
> somewhere for control features (e.g. empty features, features measuring
> a known spike-in ratio)?
> Best wishes
>  Wolfgang
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
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