Dear Gordon and all, I am having the same problem that Ulrike and Henrique were, but I don't know how to compile R for my Windows PC. Is there a somewhat easy way to do this or should I put these analyses on the back burner and wait for R 2.8.0 to be released? I appreciate any advice, Artur Veloso Hollings Marine Laboratory 331 Fort Johnson Road Charleston, SC, 29412, USA On Fri, Jul 11, 2008 at 10:14 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Dear Ulrike and Henrique, > > The problem is more likely to be with the limma normexp.fit() function than > with optim(). > > There is a rare numerical instability which causes an error like this with > normexp background correction in limma 2.14.X. Jeremy Silver and I did a > lot of work on this late last year, and we think we have eliminated the > problem. The new (faster) code is in limma on the Bioconductor > developmental repository. You can try it out if you install R 2.8.0. I'd > be interested to know if it solves the problem for your data sets. > > Best wishes > Gordon > > Date: Thu, 10 Jul 2008 17:35:51 +0200 >> From: Ulrike Goebel <ugoebel@mpiz-koeln.mpg.de> >> Subject: Re: [BioC] limma background correction >> To: bioconductor@stat.math.ethz.ch >> Message-ID: <200807101735.52255.ugoebel@mpiz-koeln.mpg.de> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Henrique, >> >> I recently got the same error with a Nimblegen dataset. Because in this >> dataset the background is actually not provided (the corresponding column >> is >> all-zero), I figured that was the reason ... However, this error occurs >> only >> with R-2.7.0, not with 2.6 or 2.5. So something must have changed in the >> optim() function (this is where it crashes in my case). >> >> Glad to hear that I am not the only one who stumbled across this ! >> >> Ulrike >> >> On Thursday 10 July 2008 17:13, Henrique Proen?a wrote: >> >>> Hi, >>> >>> I am trying to analyze some quantarray files using limma Guide, when >>> suddenly it gives me the following error at the background normalization >>> step (using normexp method and offset = 50) >>> >>> Error in if (all(abs(delta) < 1e-10)) break : >>> missing value where TRUE/FALSE needed >>> >>> I can't find why this happens. >>> Does anyone an idea of what is happening? >>> >> >> -- >> Dr. Ulrike Goebel >> Bioinformatics Support >> Max-Planck Institute for Plant Breeding Research >> Carl-von-Linne Weg 10 >> 50829 Cologne >> Germany >> +49(0) 221 5062 121 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Artur, R 2.8.0 is available pre-compiled for Windows, so you can install it anytime as you did with R 2.7.X. The current version is available from the University of North Carolina: http://mirrors.ibiblio.org/pub/mirrors/CRAN/bin/windows/base/R-2.8 .0dev-win32.exe or from http://cran.at.r-project.org/bin/windows/base/R-2.8.0dev-win32.exe Best wishes Gordon On Wed, 27 Aug 2008, Artur Veloso wrote: > Dear Gordon and all, > > I am having the same problem that Ulrike and Henrique were, but I don't know > how to compile R for my Windows PC. Is there a somewhat easy way to do this > or should I put these analyses on the back burner and wait for R 2.8.0 to be > released? > > I appreciate any advice, > > Artur Veloso > Hollings Marine Laboratory > 331 Fort Johnson Road > Charleston, SC, 29412, USA > > On Fri, Jul 11, 2008 at 10:14 PM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> Dear Ulrike and Henrique, >> >> The problem is more likely to be with the limma normexp.fit() function than >> with optim(). >> >> There is a rare numerical instability which causes an error like this with >> normexp background correction in limma 2.14.X. Jeremy Silver and I did a >> lot of work on this late last year, and we think we have eliminated the >> problem. The new (faster) code is in limma on the Bioconductor >> developmental repository. You can try it out if you install R 2.8.0. I'd >> be interested to know if it solves the problem for your data sets. >> >> Best wishes >> Gordon >> >> Date: Thu, 10 Jul 2008 17:35:51 +0200 >>> From: Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de=""> >>> Subject: Re: [BioC] limma background correction >>> To: bioconductor at stat.math.ethz.ch >>> Message-ID: <200807101735.52255.ugoebel at mpiz-koeln.mpg.de> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Henrique, >>> >>> I recently got the same error with a Nimblegen dataset. Because in this >>> dataset the background is actually not provided (the corresponding column >>> is >>> all-zero), I figured that was the reason ... However, this error occurs >>> only >>> with R-2.7.0, not with 2.6 or 2.5. So something must have changed in the >>> optim() function (this is where it crashes in my case). >>> >>> Glad to hear that I am not the only one who stumbled across this ! >>> >>> Ulrike >>> >>> On Thursday 10 July 2008 17:13, Henrique Proen?a wrote: >>> >>>> Hi, >>>> >>>> I am trying to analyze some quantarray files using limma Guide, when >>>> suddenly it gives me the following error at the background normalization >>>> step (using normexp method and offset = 50) >>>> >>>> Error in if (all(abs(delta) < 1e-10)) break : >>>> missing value where TRUE/FALSE needed >>>> >>>> I can't find why this happens. >>>> Does anyone an idea of what is happening? >>>> >>> >>> -- >>> Dr. Ulrike Goebel >>> Bioinformatics Support >>> Max-Planck Institute for Plant Breeding Research >>> Carl-von-Linne Weg 10 >>> 50829 Cologne >>> Germany >>> +49(0) 221 5062 121 >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >