Question: limma background correction
0
gravatar for Henrique Proença
11.4 years ago by
Henrique Proença80 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? -- regards Henrique Proen?a
limma • 501 views
ADD COMMENTlink modified 11.4 years ago by Gordon Smyth39k • written 11.4 years ago by Henrique Proença80
Answer: limma background correction
0
gravatar for Ulrike Goebel
11.4 years ago by
Ulrike Goebel110
Ulrike Goebel110 wrote:
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
ADD COMMENTlink written 11.4 years ago by Ulrike Goebel110
Answer: limma background correction
0
gravatar for Gordon Smyth
11.4 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k 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
ADD COMMENTlink written 11.4 years ago by Gordon Smyth39k
Dear Gordon, I have tried the 2.15.10 version of limma with R 2.8.0 and it works fine for the data set that previously gave errors. Thanks a lot for your help. Regards Henrique Proen?a -------------------------- Gordon K Smyth 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 >
ADD REPLYlink written 11.4 years ago by Henrique Proença80
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