[BioC] Limma - error when using duplicateCorrelation - Windows ver. Linux

[Gordon Smyth]

Dear Jakob,

This doesn't necessarily mean that there's 
anything wrong with your linux installation, and 
the limma versions for Windows and linux are 
identical. There are differences in floating 
point arithmetic between different hardward 
architectures, and you've run into a flag in one 
of the Lapack routines which apparently doesn't get tripped under Windows.

You could try to identify which probe, or maybe 
probes, is causing the error in linux and remove 
it from the fit. Or else you could simply use the 
duplicateCorrelation consensus correlation you got from Windows.

Best wishes
Gordon

>[BioC] Limma - error when using duplicateCorrelation - Windows ver. Linux
>Jakob Hedegaard Jakob.Hedegaard at agrsci.dk
>Tue Jan 16 15:19:38 CET 2007
>
>Hi List
>
>When using duplicateCorrelation in Limma running 
>under Linux I am receiving the following error:
>
> > cor <- duplicateCorrelation(MA, design=design, ndups=2, weights=MA$weights)
>Error in La.svd(QtZ, nu = mq, nv = 0) : error 
>code 1 from Lapack routine 'dgesdd'
>
>Interestingly, there are no problems when 
>analysing the same dataset in Limma running 
>under Windows indicating a problem with the Linux version/installation....
>
>- any suggestions would be appreciated!
>
>Linux:
> > sessionInfo()
>Version 2.3.1 (2006-06-01)
>x86_64-unknown-linux-gnu
>
>attached base packages:
>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>[7] "base"
>
>other attached packages:
>  statmod    limma
>  "1.2.4" "2.7.10"
> >
>
>Windows:
> > sessionInfo()
>Version 2.3.1 (2006-06-01)
>i386-pc-mingw32
>
>attached base packages:
>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
>[7] "base"
>
>other attached packages:
>  statmod    limma
>  "1.2.4" "2.7.10"
> >
>
>
>
>Best regards
>
>Jakob Hedegaard
>Project scientist
>
>
>UNIVERSITY OF AARHUS
>Faculty of Agricultural Sciences
>Research Centre Foulum
>Dept. of Genetics and Biotechnology
>Blichers Allé 20, P.O. BOX 50
>DK-8830 Tjele