[BioC] NUSE lmFit fitPLM

[Gordon K Smyth]

Dear Bill,

NUSE is a quality measure that is specific to the particular probe-set 
structure of Affymetrix arrays.  It depends on the fact that Affy arrays 
have a large (and constant) number of short probes for each gene. There is 
no corresponding quality measure for Agilent microarrays, which typically 
have one long probe for each gene.

Best wishes
Gordon

> Date: Thu, 12 Apr 2012 16:24:22 +0200
> From: BIll Fends <billfend at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] NUSE lmFit fitPLM
>
> Dear All,
>
> I would like to compute the NUSE (Normalized Unscaled Standard Errors) from
> agilent microarray data.
>
> Since the way I've found to do this is to use affyPLM library, using fitPLM
> function, which require an affyBatch object, I was wondering if there is
> any possibilities to use lmFit from LIMMA package to achive this goal ?
>
> I could also create an affybatch object using my agilent data but still, I
> would rather have a function which take RGList (or MAList) object instead
> of affyBatch.
>
> Is there a way to model probes and array effect using lmFit  ?
>
>
> Many thanks by advance
>
> --
> Bill Fends
>

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