[BioC] [limma] 0 weights = removed from analysis?

Gordon K Smyth smyth at wehi.EDU.AU
Thu Aug 25 01:10:12 CEST 2011

Yes, the limma manual means what it says.

Best wishes

> Date: Tue, 23 Aug 2011 17:17:44 GMT
> From: mjonczyk at biol.uw.edu.pl
> To: bioconductor at r-project.org
> Subject: [BioC] [limma] 0 weights = removed from analysis?
> Message-ID: <201108231717.p7NHHf0g003682 at woreczko.biol.uw.edu.pl>
> Dear List Members,
> in limma manual is stated that
> "A zero weight indicates that the spot should be ignored in all analysis as
> being unreliable".
> lmFit function uses information from weights.
> Is that means that zero-weight spots will not be used in functions:
> contrasts.fit, eBayes, decideTests and topTable? I.e. is zero-weight spot
> treated as having missing values for fluorescence in these functions?
> Best Regards,
> Maciej Jończyk, MSc
> Department of Plant Molecular Ecophysiology
> Institute of Plant Experimental Biology
> Faculty of Biology, University of Warsaw
> 02-096 Warszawa, Miecznikowa
> 1

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