[BioC] Standard error in summarization ExpressionSets

[James W. MacDonald]

Hi Rodrigo,

Rodrigo Santamaría Vicente wrote:
> Hi there!,
> After performing normalization-summarization with any of the available 
> functions (rma, mas5, plier, etc.), I get an ExpressionSet class. It 
> inherits from eSet class, but it seems to loss the se.exprs() method to 
> get the standard errors for the summarized expression levels.
> My question is: how could I get the standard errors from the 
> ExpressionSet returned by rma, mas5 or any other method? if these 
> methods do not return standard errors, why? are them unimportant? is 
> there any method that computes them?

None of the methods you mention return standard errors. If you want 
standard errors, you might use the affyPLM package. For instance the 
fitPLM() function will return values very similar to rma(), but with 
standard errors.

Best,

Jim


> 
> Thanks in advance!
> Rodrigo
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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