[R] Help with error

From: Gretchen Heavner <glh33_at_cornell.edu>
Date: Tue, 15 Jun 2010 11:55:17 -0400


Hi. I am trying to do a nonlinear regression on a set of data with Monod kinetics and Haldane inhibition. I am using the following commands to do the nonlinear regression:

dce<-read.delim("data.txt", header = TRUE, sep = "\t", quote="\"", dec=".", fill = TRUE, comment.char="")
dce.m1<-nls(rate~kmax*conc/(Ks+conc+((conc^2)/Ki),data=dce ,start=list(Ks=1000,kmax=6000,Ki=10000),trace=TRUE)

I get reasonable answers for Ks, kmax and Ki from this. However, I want to find the 95% confidence intervals for each of these values. So I first use the command profile:

(pr <- profile(dce.m1))

And then I ususally use the following command to get the confidence intervals:

confint(pr, level=0.95)

However, when I run the profile command, I am getting the following error:

Error in prof$getProfile() : singular gradient

Do you have any idea what this means, or what I can do to fix it? I have attached the corresponding file with the data I'm using in case that helps.

Thanks!
Gretchen Heavner



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