Thank you for the suggestions. Just to clarify, my first question was more on what actual coding I should be using to indicate a nested variable when using the coxph() function. I asked this after consulting several times with a local statistician, but unfortunately neither of us are very familiar with R.
After further consultation, I have changed the design to a 2*2 design (2 levels of ExpTemp and Stability each) with blocking (Period). I am still getting the "x matrix deemed to be singular" error. > LOEmod3alt=coxph(LOE.fit~ExpTemp+Stability+Period,data=goodexp) Warning message: In coxph(LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) : X matrix deemed to be singular; variable 5 > summary(LOEmod3alt) Call: coxph(formula = LOE.fit ~ ExpTemp + Stability + Period, data = goodexp) n= 184, number of events= 105 coef exp(coef) se(coef) z Pr(>|z|) ExpTemp -3.17825 0.04166 0.53105 -5.985 2.17e-09 *** StabilityStatic -0.84129 0.43115 0.20470 -4.110 3.96e-05 *** PeriodB 1.06794 2.90937 0.22859 4.672 2.98e-06 *** PeriodC 1.23853 3.45054 0.58457 2.119 0.0341 * PeriodD NA NA 0.00000 NA NA --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 ExpTemp 0.04166 24.0047 0.01471 0.118 StabilityStatic 0.43115 2.3194 0.28866 0.644 PeriodB 2.90937 0.3437 1.85877 4.554 PeriodC 3.45054 0.2898 1.09723 10.851 PeriodD NA NA NA NA Concordance= 0.833 (se = 0.03 ) Rsquare= 0.591 (max possible= 0.995 ) Likelihood ratio test= 164.4 on 4 df, p=0 Wald test = 111.1 on 4 df, p=0 Score (logrank) test = 179.9 on 4 df, p=0 > with(redo, table(LOEStatusfull, Period,ExpTemp)) , , ExpTemp = FIVE Period LOEStatusfull A B C D 0 42 0 35 0 1 4 0 11 0 , , ExpTemp = FOUR Period LOEStatusfull A B C D 0 0 0 0 2 1 0 46 0 44 As best as I can tell, none of my variables are collinear. Are there any other suggestions of how to deal with this error, or any more information I can provide to help understand why I would be getting this? Thank you for your time and your help, Katie On Sat, Jan 12, 2013 at 4:54 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > Katie: > > You need to get local statistical help. What you are doing makes no > sense. See inline below. > > -- Bert > > On Sat, Jan 12, 2013 at 1:03 PM, David Winsemius <dwinsem...@comcast.net> > wrote: >> >> On Jan 11, 2013, at 5:35 PM, Katie Anweiler wrote: >> >>> Hello all, >>> I am trying to understand how to specify nested factors when using >>> coxph(), and if it is appropriate to nest these factors in my >>> situation. >>> In the simplest form, I am testing two different temperatures, with >>> each temperature being performed twice in different experimental >>> periods (e.g. Temp5 performed in Period A and C, Temp4 performed in >>> Period B and D) > > Period is confounded with temperature. That is the source of the > singularity. in the message received below. > > You can estimate the C-A and the D-B differences. > As I said, get statistical help. These are not R questions. > > -- Bert > > >>> I am trying to see if survival time is affected by the treatment >>> temperature. To do this I am using temperature and experimental >>> period nested within temperature as factors. >>> >>>> LOEtempmod.5days=coxph(LOE.stable.5days~Temp+Temp/Period,data=goodstable) >>> >>> Warning message: >>> In coxph(LOE.stable.5days ~ Temp + Temp/Period, : >>> X matrix deemed to be singular; variable 2 5 6 7 >>> >>> 1. Is this an appropriate way of nesting? >> >> >> Have you looked at the coxme package? >> http://cran.r-project.org/web/packages/coxme/index.html >> >>> 2. Can this error message be ignored? >> >> >> Sometimes R packages correctly drop variables that are exactly collinear: >> other times the correct solution is not clear. I would think the answer in >> this case would be "no", but do not have a lot to go on at this point. >> >> -- >> >> David Winsemius, MD >> Alameda, CA, USA >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > > -- > > Bert Gunter > Genentech Nonclinical Biostatistics > > Internal Contact Info: > Phone: 467-7374 > Website: > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.