[BioC] Coercing Normalized Data to exprSet

Barry Henderson barry.henderson@ribonomics.com
Wed, 5 Feb 2003 08:39:49 -0500


Once I have the exprSet created with all the covariates I'll get back in
touch with you regarding the test statistic and filters.


-----Original Message-----
From: Vincent Carey 525-2265 [mailto:stvjc@channing.harvard.edu] 
Sent: Tuesday, February 04, 2003 1:44 PM
To: Barry Henderson
Cc: Vincent Carey 525-2265
Subject: RE: [BioC] Coercing Normalized Data to exprSet

> Vince, thanks for responding.
> You are correct in that I am asking "How do I use the covariate 
> information in the "experiment Cy3" and "Experiment Cy5" phenoData 
> slots to filter and test."
> In coercing a marrayNorm object into an exprSet it is just not obvious

> to me how to proceed---R is a second language.  The log ratios 
> represent 2 samples, not one, and operating on multiple covariates 
> simultaneously sounds pretty nasty.  Would it not be better if the 
> coersion method kept the samples separate in this case?  I am 
> appending one full loop as Read into my sample so you can see the 
> relationships better.  Thanks for your input.

Now that I have seen the dialogue with Wolfgang, it looks
as if you have an alternative coercion that gets you
the separate channel data.  So the problem remains to
craft a filter or test function that computes
the contrasts you are interested in.

It seems that the new("exprSet" ... expression that
was given needs to be expanded a bit so that the appropriate phenoData
are attached, and in fact those phenoData need to be created.

I have to run off for a little while but if in the mean
time you get a chance to write down the gene-specific
test statistic you would like to compute on the basis of the loop,
getting the pheno data and writing the filter will be pretty