Limma - error when using duplicateCorrelation - Windows ver. Linux
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@gordon-smyth
Last seen 13 hours ago
WEHI, Melbourne, Australia
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 All? 20, P.O. BOX 50 >DK-8830 Tjele
Genetics probe limma Genetics probe limma • 772 views
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