Hi Naomi, >[BioC] | Correlation | > 1 (limma) >Naomi Altman naomi at stat.psu.edu >Sat Nov 12 20:54:37 CET 2005 > >I just used intraspotCorrelation as suggested in the online Limma >documentation for single channel analysis. >Over half of my estimated correlation coefficients are bigger than >1.0 in absolute value. > >Naomi S. Altman 814-865-3791 (voice) >Associate Professor >Dept. of Statistics 814-863-7114 (fax) >Penn State University 814-865-1348 (Statistics) >University Park, PA 16802-2111 Just to make it confusing :) the correlations are stored on the atanh (unconstrained) scale. To get correlations on the usual scale, > corcoef <- tanh( corfit at all.correlations ) Cheers Gordon

Thank you for the clarification. The documentation does say that. --Naomi At 12:17 AM 11/13/2005, Gordon Smyth wrote: >Hi Naomi, > >>[BioC] | Correlation | > 1 (limma) >>Naomi Altman naomi at stat.psu.edu >>Sat Nov 12 20:54:37 CET 2005 >> >>I just used intraspotCorrelation as suggested in the online Limma >>documentation for single channel analysis. >>Over half of my estimated correlation coefficients are bigger than >>1.0 in absolute value. >> >>Naomi S. Altman 814-865-3791 (voice) >>Associate Professor >>Dept. of Statistics 814-863-7114 (fax) >>Penn State University 814-865-1348 (Statistics) >>University Park, PA 16802-2111 > >Just to make it confusing :) the correlations are stored on the >atanh (unconstrained) scale. To get correlations on the usual scale, > > > corcoef <- tanh( corfit at all.correlations ) > >Cheers >Gordon > Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

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That should have been: > corcoef <- tanh( corfit$all.correlations ) Gordon