Need to replicate Boltzman Signmodial Curve fit from Graph Pad
Sorry. I left out a line:
pHvals <- seq(min(dta$pH), max(dta$pH), length.out=100)
Should be inserted just before the lines() function. ------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 From: J J [mailto:rnoobier at gmail.com] Sent: Tuesday, April 23, 2013 6:49 PM To: David Carlson Subject: Re: [R] Need to replicate Boltzman Signmodial Curve fit from Graph Pad Thank you David! That looks really close, I believe Graphpad gave a V50 of ?7.244. One thing I missed on your example was where you obtained 'pHvals' from?
On Tue, Apr 23, 2013 at 5:17 PM, David Carlson <dcarlson at tamu.edu> wrote:
You may want to compare R's four point logistic with the results you get using Graphpad. For these data the Bottom parameter is not significantly different from zero (so the three point sigmoid might be adequate), but as Bert points out, especially with only 8 data points, it is probably overfitting the model.
dta <- read.table(text="pH counts
+ 3.8 968 + 5.0 1347 + 5.8 2867 + 6.6 9203 + 7.0 15817 + 7.4 20297 + 8.2 31916 + 9.2 35756", + header=TRUE)
Sig.nls <- nls(counts~SSfpl(pH, Bottom, Top, V50, Slope), dta) summary(Sig.nls)
Formula: counts ~ SSfpl(pH, Bottom, Top, V50, Slope) Parameters: ? ? ? ? ? Estimate ?Std. Error t value ? ? Pr(>|t|) Bottom ? 718.76871 ? 579.25327 ? 1.241 ? ? 0.282463 Top ? ?36983.98871 ?1008.31727 ?36.679 0.0000032986 *** V50 ? ? ? ?7.24930 ? ? 0.05054 143.436 0.0000000142 *** Slope ? ? ?0.55582 ? ? 0.05023 ?11.065 ? ? 0.000379 *** --- Signif. codes: ?0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 767.1 on 4 degrees of freedom Number of iterations to convergence: 0 Achieved convergence tolerance: 0.000003808
options(scipen=5) confint(Sig.nls)
Waiting for profiling to be done... ? ? ? ? ? ? ? ? 2.5% ? ? ? ? 97.5% Bottom ?-963.4106068 ?2243.7154750 Top ? ?34499.9962176 40150.4114887 V50 ? ? ? ?7.1173103 ? ? 7.4033391 Slope ? ? ?0.4382893 ? ? 0.7114438
coef(Sig.nls)
? ? ? ?Bottom ? ? ? ? ? Top ? ? ? ? ? V50 ? ? ? ? Slope ? 718.7687104 36983.9887074 ? ? 7.2493032 ? ? 0.5558236
plot(dta, pch=16) lines(pHvals, predict(Sig.nls, data.frame(pH=pHvals)), col="red")
------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Bert Gunter Sent: Tuesday, April 23, 2013 12:04 PM To: John Kane Cc: r-help at r-project.org; J J Subject: Re: [R] Need to replicate Boltzman Signmodial Curve fit from Graph Pad I think you'll find that this is just an alternate parameterization of a 4 P logistic. ... and in any case there is no statistically detectable difference between the two. That is, this is just basically a Graphpad marketing ploy. Fit such data with anyone's logistic function ... and that is probably overfitting in many cases, anyway. Cheers, Bert
On Tue, Apr 23, 2013 at 9:54 AM, John Kane <jrkrideau at inbox.com> wrote:
No idea of the area but does this link help? http://bioinformatics.oxfordjournals.org/content/24/13/1549.full John Kane Kingston ON Canada
-----Original Message----- From: rnoobier at gmail.com Sent: Tue, 23 Apr 2013 10:55:59 -0400 To: r-help at r-project.org Subject: [R] Need to replicate Boltzman Signmodial Curve fit from Graph Pad Hello useRs (please don't kill me), I've fairly new to R having only a few months of playing around with R. What little I've learned has been extremely useful. If someone could point me as to how to replicate the Boltzman Sigmodial curve fit as provided by Graphpad software I'd be eternally
grateful.
Where ?we currently use Graphpad for only this one function,its seems highly inefficient for a $100 piece of software to be used for only one function (which isn't nearly as bad as the company's pandemic reliance on Excel for nearly everything else). so anyway, what I'd normally do is take a set of data like this: ?pH counts ?3.8 968 ?5.0 1347 ?5.8 2867 ?6.6 9203 ?7.0 15817 ?7.4 20297 8.2 31916 ?9.2 35756 then fit this to a Boltzman sigmodial in Graphpad. Graphpad spits out a much longer set of vectors and also information about v50 and confidence intervals etc (if anyone is familiar with that software). This is what i'd like to replicate. It might be that I just don't know what i'm doing,so feel free to call me an idiot but any help is greatly appreciated! -JJ ? ? ? [[alternative HTML version deleted]]
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-- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biost atistics/pdb-ncb-home.htm ______________________________________________ R-help at 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.