The dose-response equations built-in to Prism all assume that the X values are log(dose). You can either enter the data with X values as logarithms of doses, or use the Transform analysis to create a results table with the data arranged that way which can then be graphed and fit. 

It is possible to fit data where X values are concentrations, rather than log(concentrations). It is necessary to adjust the equation accordingly. 

Here is the equation built-in to Prism for fitting a variable slope (four-parameter) log(dose) response curve:

   Y=Bottom + (Top-Bottom)/(1+10^((LogEC50-X)*HillSlope))

Here is the equation modified to expect X values to be concentrations, not logarithms, so the concentration does not need to be raised to the tenth power to antilog it:

  Y=Bottom + (Top-Bottom)/(1+ (10^logEC50 /X)^HillSlope)

The equation still fits the logEC50, rather than the EC50. Why? Because the confidence intervals computed by Prism are always symmetrical around the parameter value. But the true uncertainty is only symmetrical on a logEC50 scale.  

Download this Prism file to see how it works. The same data are fit  and graphed twice.

• In one version the X values are transformed to logarithms, and then fit to the equation built-in to Prism. Here the graph has a linear X axis, but the numbering is converted to powers-of-ten to show that the X values represent logarithms.
• In the other version, the data are fit with the X values remaining as concentrations and fit to the equation showed above. Here the X axis is stretched to a logarithmic scale (top right of Format Graph dialog). 

The two graphs look identical. The results of the two fits are identical. 

Note that the second graph will only look good in Prism 5, which is smart about plotting curves on axes stretched to a logarithmic scale. Prism 4 was not smart about this, and the resulting curve looks very choppy.

Why is the HillSlope applied to the EC50 as well as the X values?

Why doesn't Prism report the standard error of the EC50?

Apple released a new version of OSX, 10.6 Snow Leopard, on Aug. 28 2009.

Prism 5

We know of one problem using Prism 5.0b on Snow Leopard: Fill patterns don't render well. We recommend that you use solid fills for bars, and simply avoid fill patterns altogether if you use Snow Leopard (and even otherwise, fill patterns are a hold over from the days of plotters, and solid fills look better). It is likely that Apple will fix this glitch in Snow Leopard. If they don't, we'll try to bypass the problem in release 5.0c. 

Other minor glitches:

• Black colors appear gray when the graph is exported to a pdf file using CMYK colors, and viewed in Preview. Choose RGB colors instead, and the pdfs look fine.  Or export a tiff file with CMYK colors. Note that the pdf file is fine, but is just rendered incorrectly by the new version of Preview.
• The Send-to-Powerpoint button and command don't work. Use Copy and Paste instead.
• When running a Prism script, the script log is always empty.
• Editing sheet names in the navigator looks ragged.
• The slider on the info page separating info constants from notes looks corrupted.
• Exporting to the PICT format doesn't work. 
• Exporting using the monochrome color model (to export colorful graphs as black and white) doesn't work.
• If you save a Prism file as XML, its icon is blank.
• One person found that the updater from 5.0a to 5.0b did not work under Snow Leopard. But the full 5.0b installer worked fine.

 We will investigate these problems, and any others we discover or are told about, and fix in release 5.0c coming soon. Let us know if you encounter other problems. 

InStat, StatMate, and Prism 4

InStat 3, StatMate 2 and Prism 4 use an older style of Mac programming. They run perfectly on current macs using an Intel chip, but do so by relying on Apple's Rosetta system. Apple created Rosetta so programs written for the earlier generation of Macs that use a PowerPC chip will also work on newer Intel Macs. This is truly amazing software that just works. You don't even know it is there.

With OSX 10.4 (Tiger) and 10.5 (Leopard), Rosetta was automatically installed and simply works when it is needed. You don't have to configure it, and won't even know when it is running. The only exception is that a few people have had problems after updating to OSX 10.5.6. This page from the Apple web site explains how to fix the problem, which requires running the 'combo update' rather than the 'incremental update' .

Rosetta is not automatically installed with  OSX 10.6 (Snow Leopard). If you are updating to Snow Leopard and plan to run InStat 3, StatMate 2, or Prism 4, click the "Customize" button in the Mac OS X Snow Leopard installer and select the option to install Rosetta. 

If you don't install Rosetta at the time you install Snow Leopard, or get a new Mac without it,  InStat, StatMate and Prism 4 will still work just fine. The first time you run one of these programs under Snow Leopard, OSX detects that you need Rosetta and provides an easy way to install it. You only have to do this once. Rosetta will be installed from Apple's server if you are connected to the internet. Otherwise, you'll need to insert your Mac OS X Snow Leopard installation disc, open the Optional Installs folder, and double-click Optional Installs.

Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Writing and Editing for Biomedical Publications is a lengthy document with guidelines for authors and publishers. But it has only one paragraph about statistics:

"Describe statistical methods with enough detail to enable a knowledgeable reader with access to the original data to verify the reported results. When possible, quantify findings and present them with appropriate indicators of measurement error or uncertainty (such as confidence intervals). Avoid relying solely on statistical hypothesis testing, such as P values, which fail to convey important information about effect size. References for the design of the study and statistical methods should be to standard works when possible (with pages stated). Define statistical terms, abbreviations, and most symbols. Specify the computer software used."

These two papers give sensible guidelines for presenting statistical calculations and conclusions:

Curran-Everett and Benos. Guidelines for reporting statistics in journals published by the American Physiological Society. AJP - Gastrointestinal and Liver Physiology (2004) vol. 287 (2) pp. G307. Those authors later published a sequel, with additional comments. This sequel references a bunch of papers which critique the guidelines.

Ludbrook. The presentation of statistics in Clinical and Experimental Pharmacology and Physiology. Clin Exp Pharmacol Physiol (2008) vol. 35 (10) pp. 1271-4). Ludbrook has also self published a two-page set of guidelines for mathematical operators and statistical symbols.  

These authors agree on two points (regarding style, not substance) that I was not aware of, so the GraphPad manuals and help screens (and my book Intuitive Biostatistics) have done differently:

• They say that the standard error of the mean should be abbreviated as SE, rather than SEM.
• They say that the mean and standard deviation should be written as mean (SD), rather than mean ± SD. if the mean is 11.2 and the standard deviation is 2.4, they suggest reporting 11.2 (2.4) rather than 11.2  ± 2.4. They recommend using that latter syntax only for standard errors, not standard deviations.