Prism offers many choices on its Preference dialog. Beyond that, it remembers which files you have recently opened or closed, user-defined equations you have created, color schemes you have created, autocomplete text, and more. All that is saved in a preference file. This means that Prism is customized for you. 

When Prism is used in a teaching lab, this customization is not helpful. When a student uses Prism, preferences set by other students will be used, and it may seem that Prism acts unpredictably.

To make Prism start up exactly the same each time, write-protect the preference file. Details here.

 A single-phase exponential decay curve will plot as a straight line when the Y-axis is logarithmic only if the curve plateaus to zero. As implemented in Prism, you would need to constrain the Plateau parameter to a constant value of zero. If the plateau is not 0.0, the exponential decay will look curved, even on with semi-log axes.

Similarly, as shown below (download the Prism file), a two-phase exponential decay curve will appear as two straight lines on a semi-log graph only if the plateau is constrained to zero. If the plateau is not zero, both components will looked curved, even with a logarithmic Y-axis.

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Problem: All values paste into one cell

If you double clicked on a cell in Numbers or Excel, then there will be a flashing insertion point to indicate that you are in edit mode. All values in the clipboard will paste into that one cell. This is frustrating because the appearance of edit mode is so subtle. Look for the insertion point. Excel works the same way, but it is much more obvious when you are in the edit mode, as the selected cell is shown with a drop shadow, giving a 3D look.

Instead, single click on a cell before pasting. The cell will have a border to show it is selected, but  there will be no flashing insertion point. Now, each value will paste into its own cell, starting at the spot you selected. Numbers and Excel work the same way. 

Problem: Only a portion of the copied values paste

If you selected a range of cells in Numbers, then each value will paste into its own cell within that range. If the table copied to the clipboard is longer or wider than the region you selected in Numbers, some values won't paste. In contrast, Excel will paste beyond the selected range to paste all the values on the clipboard. 

  

 

 When you open a file from a temporary folder, Prism 5 is smart. When you click Save, it doesn't just save to that temporary folder. Instead it opens the Save As dialog, so you can save it to a proper (not temporary) folder. This usually makes sense, as there is a good chance the file came from an email and you didn't really want to save back to the temporary folder.

But, we learned, some people do want to save back to the temporary folder. In particular, this makes sense when a Prism file is included in a Microsoft OneNote notebook file. When you double-click to edit, OneNote makes a temporary file and opens it in Prism. When you resave in that same temporary location, OneNote imports that temporary file back into the notebook. But Prism 5.00 and 5.01 added an extra step, popping up the Save As dialog. 

Prism 5.02 offers an option to prevent this. At the top of the File&Printer tab of Preferences is a new option:

  [x]Always prompt when saving to a temporary folder

Uncheck that option, and Prism will save back to a temporary folder (without popping up any dialog) when you click Save. 

The Prism Mac 5.0b updater, as its name suggests, updates Prism Mac 5.0a to 5.0b.  What's new?

While the updater usually works perfectly, occasionally it can hit a snag. If it doesn't work for you, these tips might help:

• The updater expects to find Prism 5.0a in a folder named "Prism 5" within the Applications folder. If you have renamed that folder, the updater won't find it. But you can specify the new location/name in the top of the third step of the updater.
• The updater expects the Prism 5.0a application to be named "Prism.app". If you have renamed it, rename it back.
• If Prism 5.0a is running while the updater works, all the files will be updated and you won't see any warning. But when the update is done, Prism 5.0a will still be running.  Quit Prism and then launch it again to use Prism 5.0b. 
• If you have set the Prism folder or application to have "No access" in the Sharing and Permissions section of Get Info, set it back to Read only or Read&Write.

If these tips don't help (or you don't want to bother with them) email us to  request a link to a full installer (rather than updater). Include your serial number with the request. 

When you copy data from Excel and paste into Prism (Windows only, version 3 or later), Prism offers three choices in a secondary menu:

• Paste Data -- Prism retains no link back to the Excel spreadsheet. The values will be pasted and nothing else. The only advantage to using this method is that it is conceptually the simplest.
• Paste Embed -- You paste the selected data into the data table and also paste a copy of the entire spreadsheet file into your Prism project, even if it has several worksheets (tabs). This means you don’t need to worry about keeping track of multiple files. You don't need to save the spreadsheet file separately (except as a backup). You can open Excel from within Prism, edit the data, and instantly update the analyses and graphs in Prism. A potential disadvantage of embedding is that you will end up with multiple copies of the same data (some see this as an advantage). Another disadvantage is that your Prism files will be larger.
• Paste Link -- Paste the values into the data table but also create a link back to the Excel file. The link has two functions. It lets you trace (and document) the source of the data so you stay organized. It also is a live link. If you edit or replace the data within Excel, Prism will update the analyses and graphs. The Paste Link command is available only if you paste from an Excel workbook that has a name. If you are working with a new Excel file, you must first save it (thus giving it a name) before you can link its data into Prism. When in doubt, use Paste Link. The link is via the file name only. If you move the Excel file, or rename it, the link will be gone. 

Linking and embedding of Excel data into Prism are unique features that (as far as we know) no other statistics program offers.  Use Excel for organizing the data, and doing some preliminary calculations. Then copy and paste-link or paste-embed those results into Prism for further analyses and graphing.  The entire chain of calculations in both programs is easy to trace, and the entire chain will update if you edit or replace the data in Excel. 

Notes:

• With Prism Mac, you can only paste values. The Macintosh system does not have the infrastructure needed to link or embed Excel files. 
• Prism Windows also lets you import Excel files. We don't recommend this. It is better to copy selected portions of the Excel file and then paste, paste-link, or paste-embed into Prism.
• Prism 5 actually offers seven choices when you paste Excel data: the three choices above, those same three choices performed as paste transpose (so each row becomes a column, and each column becomes a row), and paste special which gives you all of those choices and also lets you use all the options in the Import dialog (skipping rows and columns, rearranging values, etc.).
• When you paste-link or paste-embed Excel data into Prism, you won't be able to edit the data in Prism. Instead, you can double-click on that block of data to return to Excel for editing. 
• It is possible to unlink the data block from Excel.
• One Prism file can have multiple data table with data from Excel. Each data table can have multiple blocks of data individually linked to Excel (or containing different embedded Excel values). 

 

The allosteric EC50 shift model described by Christopoulos and Kenakin (Pharmacol Rev, 54: 323-374, 2002) is built in to Prism 5. It fits a family of curves, to determine the EC₅₀ of the control curve as well as two parameters (K_b and alpha) that describe the allosteric interaction of a modulator. 

The description in the Prism help neglects one important "detail": You must have at least three curves, and preferably more.

If you only have one control curve and one curve in the presence of modulator, the values of K_b and alpha are simply not defined.  An infinite combination of Kb's and alpha's can give you the same shift. The fit will be ambiguous.

For the fit to actually converge and not be ambiguous, it is necessary to define the value of the allosteric cooperativity parameter, alpha. This requires enough curves such that the progressive shifts of the agonist concentration-response curve starts to approach a limit.

New to Prism 5 is the diagnosis of an 'ambiguous' fit. This term is unique to Prism, but the idea is not novel. Prism reports 'ambiguous' when the dependency of one or more parameters is nearly 1.00.  This means that the parameters are so intertwined, that there are an infinite number of combination of parameter values that generate curves that fit equally well. The curve would fit well, but the best-fit values of the parameters are almost arbitrary.

If you choose to compare two models on the Compare tab of nonlinear regression and one or both fits is 'ambiguous', Prism 5.00, 5.01 and 5.0a does not continue with the comparison. If the fit of the other model is not ambiguous, Prism chooses that one to graph regardless of its sum-of-squares. If both fits are ambiguous, then Prism plots no curve.

If you are opening a file created by Prism 4, this means that Prism 5 may (in rare cases) plot a different model than Prism 4 did. Prism 4 fits the one with the lower sum-of-squares if the fit is enough better to be statistically significant (F test) or have a lower AICc. If one fit is ambiguous, Prism 5 picks the other model, regardless of sum-of-squares.  In some cases, Prism 5 will plot no curve even though Prism 4 did.

If the goal of the comparison is to find a scientifically plausible model, then it makes sense to avoid models with ambiguous fits, regardless of how well they fit the data. If your goal is just to plot an attractive curve, perhaps to use as a standard curve for interpolation, then plotting a model whose fit is ambiguous might make sense.

We updated Prism 5.02 (Windows) and 5.0b (Mac) to give you a new choice in the Compare tab:

[ ] If one fit is ambiguous, choose the other without formal comparison.

It is checked by default to match previous versions of Prism.

One of the pages (or 'views') in the survival analysis page is "# of subjects at risk". Since the number at risk applies to a range of days, and not to a single day, the table is a bit ambiguous. 

Here is the top six rows of that table for the sample data (comparing two groups) that you can choose from Prism's Welcome dialog. 

 

Days	Standard	Experimental
0	16	14
90	16
142	15
150	14
269	13
272		14

The experiment starts with 16 subjects receiving standard therapy and 14 receiving experimental therapy. On day 90, one of the patients receiving standard therapy died. So the value next to 90 tells you that there were 16 subjects alive up until day 90, and 15 at risk between day 90 and 142. At day 142, the next patient dies, also on standard therapy. So between days 142 and 150 (the next death), 14 subjects are at risk in the standard group. 

 

We released Prism 5.02 (Windows) and 5.0b (Mac). If you have purchased Prism 5, please update. The update is free, of course, to people who already use Prism 5.0x.

The update includes a few new features, and many fixes. Details here.

We call the update 'minor' because it doesn't add many new features. But the effort required to create these updates was not minor. GraphPad works hard to maintain Prism, and these updates incorporate about five programmer-years of hard work. Please take a few minutes to update your Prism.