[BioC] Limma and pre processing Agilent single color arrays

Gordon K Smyth smyth at wehi.EDU.AU
Sun Nov 10 11:31:46 CET 2013

Dear Amanda,

The short answer is that limma takes all the parameters that it needs from 
the Feature Extraction output.

I can't give you any more specific answer, because there is no output 
produced by the Agilent Feature Extraction software called a "flag 
measurement parameter".  limma allows you to access and use any column of 
information produced by Feature Extraction, but you need to know the name 
of the parameter that you want to use.

Generally you should not need to access anything other than what limma 
reads automatically.  Agilent arrays are usually good quality, and the 
limma procedures are robust, so agonising over outliers (if that is what 
is worrying you) is not usually necessary.

Best wishes

> Date: Thu, 7 Nov 2013 16:54:20 -0200 (BRST)
> From: amandafassis at usp.br
> To: bioconductor at r-project.org
> Subject: [BioC] Limma and pre processing Agilent single color arrays
> Dear mail list members,
> I'm working with Agilent single color arrays (4 x 44K) wich data were 
> extracted by Feature Extraction software; this software provides some 
> flags measurements in the file.
> In limma manual the authors showed an example with Agilent single color 
> arrays: Time Course E ects of Corn Oil on Rat Thymus with Agilent 4x44K 
> Arrays - but in this they filtered out control probes and low expressed 
> probes.
> I couldn't find in the manual if limma takes the flag measurement 
> parameters to process data. If not, does anyone have an example of a 
> function do to that?
> Best regards,
> Amanda Freire de Assis, MSc
> Molecular Immunogenetics Group
> University of São Paulo
> Av. Bandeirantes, 3900
> 14049-900 - Ribeirão Preto - Brazil
> +55 16 36023246

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