[BioC] [limma] Separate Channel Analysis of 2 color data with summarization

Gordon K Smyth smyth at wehi.EDU.AU
Wed Aug 11 01:45:55 CEST 2010

Dear Ana,

Your idea sounds reasonable in principle to me.  It seems reasonable to me 
that summarized values would have somewhat less tight correlation than R/G 
values on the same spot, so I wouldn't be worried about an intraspot 
correlation of 0.5.

Best wishes

> Date: Mon, 9 Aug 2010 19:02:02 +0200
> From: Ana Conesa <aconesa at cipf.es>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] [limma] Separate Channel Analysis of 2 color data with
> 	summarization
> Dear List,
> I am analyzing some yeast Nimblegen arrays following the separate channel
> analysis of 2 color data of the limma package. After within and between
> arrays normalization steps I did a summarization (medianpolish of M and A
> values for 12 spots/gene) step to reduce the number of features for
> differential expression analysis. My idea was then to calculate
> intraspotcorrelation and use the lmscFit function. My question is whether it
> should be OK to compute the intra spot correlation and the linear model using
> these summarized values. One  result that calls my attention is that the
> intraspotcorrelation computed on the summarized values has a consensus value
> of 0.517.  From other posts in the list, it has been mentioned that intraspot
> correlation should be above 0.8, so I am wondering if this approach is
> conceptually correct.
> Thanks for any suggestion on this topic
> Regards
> -- 
> Ana Conesa
> Bioinformatics and Genomics Department
> Centro de Investigaciones Principe Felipe
> Avda. Autopista Saler 16,
> 46012 Valencia, Spain
> Phone: +34 96 328 96 80
> Fax:   +34 96 328 97 01
> http://bioinfo.cipf.es/aconesa
> http://www.blast2go.org

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