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Dear Jacob, Try identifying which gene is causing the error. Edit the function duplicateCorrelation, by using fix(duplicateCorrelation), to add the line cat(i,"\n") immediately before the line y <- drop(M[i, ]) Then try running duplicateCorrelation() again. This will tell you which gene is causing the problem. Suppose the problem is at gene 10000. Looking at the data MA[10000,] may tell you what the problem is. Alternatively it might be enough to simply remove the offending gene from the duplicateCorrelation calculation by duplicateCorrelation(MA[-10000,],design) Removing one gene will not make any material different to the computed value. Best wishes Gordon > -----Oprindelig meddelelse----- > Fra: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] > Sendt: Tuesday, October 10, 2006 1:21 PM > Til: Jakob Hedegaard > Cc: bioconductor at stat.math.ethz.ch > Emne: [BioC] Limma - error when using duplicateCorrelation > > Dear Jakob, > > I've never seen this error, despite using duplicateCorrelation() often. Please provide a > reproducible example so that the error can be tracked down. > > Best wishes > Gordon > >> Date: Tue, 10 Oct 2006 09:06:20 +0200 >> From: "Jakob Hedegaard" <jakob.hedegaard at="" agrsci.dk=""> >> Subject: [BioC] Limma - error when using duplicateCorrelation >> To: <bioconductor at="" stat.math.ethz.ch=""> >> >> Hi List >> >> When using duplicateCorrelation in Limma 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' >> >> - any suggestions would be appreciated.... >> >>> 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" >> >> >> >> Best regards >> >> Jakob Hedegaard >> Project scientist >> >> >> >> Danish Institute of Agricultural Sciences Research Centre Foulum >> Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 >> DK-8830 Tjele >> >> Phone: +45 8999 1900 >> Direct: +45 8999 1363 >> E-mail: Jakob.Hedegaard at agrsci.dk <mailto:jakob.hedegaard at="" agrsci.dk=""> >> Web: www.agrsci.org <http: www.agrsci.org=""/>