[BioC] dupcor.series

Gordon Smyth smyth at wehi.edu.au
Wed Mar 17 00:52:49 MET 2004


I am a bit dubious about the merits of between array normalization when 
there are so many missing values (nearly 6000 on one of the arrays), but it 
shouldn't in principle cause an error to the duplicateCorrelation function. 
So there may be a bug in the function. Would you be prepared to send me the 
data matrix so that I can try it out myself?


At 08:38 PM 16/03/2004, Jason Skelton wrote:
>>>*Error in chol(dinfo) : the leading minor of order 2 is not positive
>>I've never seen this error either. What version of R/limma are you using? 
>>What do you see if you type
>Hi Gordon
>Using limma version 1.5.1
>& R version 1.8.0
>If I look at the normalized within Arrays data (Which works with 
> > summary(nwam0m2MA$M)
>B737.10.03.2004.m0m2.5um.0019m0m2 B737.10.03.2004.m2m0.5um.0046m0m2
>Min.   :-1.417e+01                Min.   :-1.638e+01
>1st Qu.:-1.224e+00                1st Qu.:-6.466e-01
>Median :-2.273e-03                Median : 8.657e-03
>Mean   :-2.393e-01                Mean   :-1.095e-02
>3rd Qu.: 1.105e+00                3rd Qu.: 6.254e-01
>Max.   : 7.943e+00                Max.   : 8.213e+00
>NA's   : 5.811e+03                NA's   : 1.685e+03
>The normalised between arrays data looks like this
>I can't see that much difference but the quality of the second array 
>wasn't that great in the first place.
> > summary(nbamom2MA$M)
>B737.10.03.2004.m0m2.5um.0019m0m2 B737.10.03.2004.m2m0.5um.0046m0m2
>Min.   :-1.048e+01                Min.   : -22.15456
>1st Qu.:-9.056e-01                1st Qu.:  -0.87431
>Median :-1.681e-03                Median :   0.01171
>Mean   :-1.770e-01                Mean   :  -0.01481
>3rd Qu.: 8.174e-01                3rd Qu.:   0.84567
>Max.   : 5.874e+00                Max.   :  11.10602
>NA's   : 5.811e+03                NA's   :1685.00000

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