[BioC] dupcor.series

[Jason Skelton]

>
>
>>
>> *Error in chol(dinfo) : the leading minor of order 2 is not positive
>> definite.*
>
>
> I've never seen this error either. What version of R/limma are you 
> using? What do you see if you type
>
> summary(nbaResults$M)?



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 
dupcor.series)

 > 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 
(B737.10.03.2004.m2m0.5um.0046m0m2)
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              

Cheers

Jason

-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
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