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

Hi,

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.

Best,
	Kevin

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

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber