Hello Limma Developers, I got this error when calling ebayes after lm.series: Error in ebayes(fit) : No residual degrees of freedom in linear model fits I tried both limma 1.3.1 and 1.3.12. I appreciate your help. thanks, Ken Ninh

Dear Ken, This error message is due to having too many parameters for the number of observations. You need to provide: the experiment design (i.e. how many arrays for each condition and the set of conditions) the design matrix you sent to the program Without this information, no-one can assist you. --Naomi Altman At 10:11 AM 1/16/2004, kninh@mdanderson.org wrote: >Hello Limma Developers, >I got this error when calling ebayes after lm.series: > >Error in ebayes(fit) : No residual degrees of freedom in linear model fits > >I tried both limma 1.3.1 and 1.3.12. I appreciate your help. > >thanks, >Ken Ninh > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Actually it is because the release version has a bug when you pass an exprSet to lmFit. The devel version has the fix, or you can hack the line (about line 30 or so) if(is.list(object)){ to read if(is.list(object) & !is(object, "exprSet"){ Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Naomi Altman <naomi@stat.psu.edu> 01/16/04 3:06 PM >>> Dear Ken, This error message is due to having too many parameters for the number of observations. You need to provide: the experiment design (i.e. how many arrays for each condition and the set of conditions) the design matrix you sent to the program Without this information, no-one can assist you. --Naomi Altman At 10:11 AM 1/16/2004, kninh@mdanderson.org wrote: >Hello Limma Developers, >I got this error when calling ebayes after lm.series: > >Error in ebayes(fit) : No residual degrees of freedom in linear model fits > >I tried both limma 1.3.1 and 1.3.12. I appreciate your help. > >thanks, >Ken Ninh > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hmmm, that would be the old 'didn't quite read the question closely enough but answered anyway'... Thanks for the correction Gordon. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Gordon Smyth <smyth@wehi.edu.au> 01/16/04 8:17 PM >>> Sorry, Jim, this isn't the problem here. Kninh has used lm.series, not lmFit. Gordon At 12:00 PM 17/01/2004, James MacDonald wrote: >Actually it is because the release version has a bug when you pass an >exprSet to lmFit. The devel version has the fix, or you can hack the >line (about line 30 or so) > >if(is.list(object)){ > >to read > >if(is.list(object) & !is(object, "exprSet"){ > >Best, > >Jim > > > >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > >>> Naomi Altman <naomi@stat.psu.edu> 01/16/04 3:06 PM >>> >Dear Ken, >This error message is due to having too many parameters for the number >of >observations. You need to provide: > >the experiment design (i.e. how many arrays for each condition and the >set >of conditions) >the design matrix you sent to the program > >Without this information, no-one can assist you. > >--Naomi Altman > > >At 10:11 AM 1/16/2004, kninh@mdanderson.org wrote: > > > >Hello Limma Developers, > >I got this error when calling ebayes after lm.series: > > > >Error in ebayes(fit) : No residual degrees of freedom in linear model >fits > > > >I tried both limma 1.3.1 and 1.3.12. I appreciate your help. > > > >thanks, > >Ken Ninh _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor