What's new in GraphPad Prism Mac 6.0d?

This page lists the changes in Prism Mac from 6.0c to 6.0d (which began beta testing in July 2013). If you are updating from an earlier release, see what was new in 6.0b and 6.0c

This page is for Mac only. A seperate page lists what's new in 6.03 Win.

New features

  • Works great with OSX 10.9, Mavericks. See changes. Earlier releases will run under Mavericks if already installed, but cannot be installed on a Mavericks computer.
  • You can choose symbol shape, border color and border thickness for outliers in box-whisker graphs.
  • The Delete Sheet dialog is wider so you can see long sheet names, and taller so there is less need to scroll.
  • You can choose to plot symbols at censored points only for survival graphs showing staircase with ticks.
  • Reports sample size of each group in the results of Mann-Whitney test.
  • Improved labeling of hazard ratio (and its reciprocal) in survival analysis.
  • If you choose not to open a file when you quit Prism, Prism still saves a backup (unless you set Preferences not to), and when you open that file, Prism now gives you a choice of whiich version of file to open: auto-saved or manually saved version.
  • You can to mail sheet/project/family under OS 10.7.

Important analysis bugs fixed

  • The Wilcoxon rank sum test is a nonparametric test that is part of the column statistics analysis that compares the computed median with a theoretical value you enter. Prism 6.02 (Windows) and 6.0c (Mac) introduced an bug such that the P value was always reported P<0.0001. This bug was not in 6.00, 6.0a, 6.01, or 6.0b, and is fixed in 6.03 and 6.0d. 
  • The Wilcoxon matched paris test (part of t test analysis) was incorrect when you chose to use method of Pratt to handle the rare situation where the two values were equal in some rows.
  • Comparing three or more survival curves using the Gehan-Wilcoxon survival method gave incorrect results. (Comparing two data sets was always fine.) 

Other analysis bugs fixed

  • All the equations in the Binding Kinetics family of equations will now, by default, plot curves begininning at X=0 rather than the minimum X value in the data table.
  • In very rare circumstances, nonlinear regression can show the initial values as the results, with no message that there was a math error.
  • When frequency distribution is done with grouped data and each replicate is individually binned, the column statistics show the column statistics of the means, not of individual replicates. But the sample size n was reported as the total number of replicates, but is now correctly reported as the number of means used to compute the grand mean and SD etc. 
  • Median Survival is reported incorrectly for a data table that has some X values occur several times on the table without corresponding Y values, and when the curve was horizontal at Y=50%, making the concept of a single value for median survival quite arbitrary.
  • X and Y values were swapped in Interpolated X values result subsheet of the Fit spline analysis.
  • Mann Whitney test would crash/freeze with huge data sets (hundreds of thousands of values).
  • Improved computation of critical values of t distribution used for confidence intervals. Difference is usually only in the fifth digit of precision, but occasionally is in the third or fourth digit.
  • In rare cases, a simulated curve generated from a model defined with a differential equation periodically dropped to zero.
  • In very rare circumstances, nonlinear regression would show the initial values as the results, with no message that there was a math error.  
  • Changed '(recommended)' next to the Pratt option to '(not commonly used)' when choosing the Wilcoxon signed rank test in Column statistics.

Important bugs fixed

  • Crash when opening a layout that includes a graph that includes embedded table. Details.
  • Freeze or crash after opening a file that contains a data table with several data objects pasted as links.
  • XY points with X values equalling the axis limits were not shown on the graph.
  • Crash when trying to resize the graph using either the Change menu or Resize Graph by right clicking.
  • The scale factor for graphs on the layout sometimes differed from Win Prism version, which meant the graphs didn't quite align.
  • Error bars pointing down from negative bars were plotted all the way to the axis.

Changes in installation, activation and startup

  • If silent activation is configured and the IT admins have updated the xml with a new serial number before the expiration date, Prism will silently use it without showing any dialogs.
  • When a serial number expires, Prism now display a dialog with the choices to enter a new number, go to our website, or quit.
  • Changed Prism so that if <check-for-updates> exists in startupconfig.xml, then Prism disables the corresponding check box in the preferences dialog.
  • Fixed misleading silent activation error message when connection to the GraphPad server works fine but the server returns an error.
  • Improved the error message (code XX) when Prism detects that the system clock has been tampered with.
  • Prism now only contacts the LabArchives server when needed, instead of every time Prism starts.
  • With activation, Prism now sends the version number to the GraphPad server.
  • New alert if user tries to enter a masked serial number (using ### instead of actual numbers).
  • Dialog that warns of expiration in next 30 days now offers place to enter the replacement serial number to make it easier to handle renewal.
  • New choice to activate for all users on the computer (requires password) or just for the current user (no password needed).

Other fixes

  • Characters <, >, " and & copied from MS Excel appeared as <, >, " and & when pastedinto column titles.
  • The 'Change Graph Type' dialog appeared with incorrect default graph family when switching to graph, if it had already been viewed before data was entered.
  • The graph/axis title appeared truncated up to the last existing '%' character, if it was being set via script command inside loop.
  • Pasting into an Info sheet table was truncated if some of the values included comma separator.
  • Graph was exported as a small image or invisible if some of the groups had column title but no data.
  • Fixed broken help links for two-way ANOVA and other.
  • Duplicating family automatically updated the sheet name only for the first linked graph but not the other linnked graphs.
  • Removed automatic gray floating note incorrectly saying that some error bars were clipped at the axis limit.
  • Removed unnecessary column titles from the Two-way ANOVA results sheet.
  • Removed unexpected extra lines that were plotted on the graph with two segments for X axis.
  • Graph legend sometimes disappeared when Prism 5 file opened on Prism 6.
  • Removed duplicated sample data set in Grouped tab.
  • Equal size graphs placed on equal size layout placeholders sometimes had slightly different scaling factors on layout so didn't match.
  • Fixed the spacing between the X axis and bottom of bars after dragging bottom of the Y axis down with offset axes.
  • Axis numbering with log or antilog didn't obey setting for number of decimals to show.
  • The color for symbols was incorrectly applied to a curve.
  • Fixed the swiping and scrolling depending on the settings in the System preferences with Magic mouse or trackpad.
  • Data tables embedded on a graph sheet were located overlapped the page boundary.
  • Included the mean value in the tooltip shown for bars of the column graphs.
  • "Cannot open file" alert appeared on opening a particular file that contains an invisible one-way ANOVA analysis.
  • Made Prism plot the error bars and symbol, if an X value is exactly at the minimum (or maximum) of the axis range.
  • If you wanted to choose different colors for different data ranges selected on the table, you had to close the color chooser after each choice to make it stick.
  • If you choose on Format Axis "No left Y axis", the right Y axis was then moved to the left.
  • Activation of an expiring license required admin rights.
  • Pasting bitmap images would sometimes be at 72dpi when it should be 150 dpi (noted with drawings from EasyDraw). 
  • Tab keys didn't work properly to switch between tabs in "Format Axes" dialog/
  • When duplicating a family with several graphs, only the graph title of the first graph was updated.
  • Improved the auto-recovery of files with damaged sheets.
  • Prism would freeze when you open a project where 0 is plotted on logarithmic axis (Mac OS 10.7 and later).
  • Some files would not open when the layout sheets used some custom paper sizes.
  • No longer freezes when opening a project which includes 0 value plotted on logarithmic axis, or with unusual custom page sizes.
  •  It was impossible to format individual symbols and error bars on grouped graphs showing individual values via contextual menu in data table.
  • The 'Position Object' command for axis titles is now disabled, since they are automatically centered on the axis.
  • Choices in Font palette, invoked from 'Format Axes' dialog, were not updated when you changed several fonts before clicking OK.
  • If you selected text while the Font Panel is open, the font panel would not update to show the font of the current selection.
  • Labels for additional ticks on the x-axis were not always aligned properly.
  • Some graphs were not shown (only gray background appeared) when the default was to use certain custom paper sizes.
  • Custom range of X axis was calculated incorrectly if row titles were used for labeling.
  • On the welcome dialog (or Format Data Table dialog) you can enter the number of replicates for XY or grouped graphs. But it was not possible to enter any number starting with 1.
  • When you copied an entire column of data on one table and paste linked to another table, Prism was really slow. Now it is much faster.
  • On some graphs, it was not possible to stretch the X axis.
  • When data were plotted with a logarithmic Y axis, Prism got confused when the length of the error bar was greater than the mean (so the downward pointing error bar is impossible to plot).  
  • Magic (make graphs consistent) wouldn't change the color of connecting lines.
  • The "Show tooltips" preferences choice did not apply immediately - only after switching sheets.
  • The "Column 0" argument of script commands did not refer to the Row Title column (as they should) if there was no X column in the table.
  • Snapping of X axes did not work on layout page.
  • Clicking on the disclosure triangle in front of Results folder did not expand results sheets list when Data with results section was open. 
  • Navigating within data with results section sometimes didn't work after performing analyses.
  • Long labels on a graph were incomplete on layout.
  • Edits to XY tables with row titles but no X values didn't always show in the graph.
  • Font sizes, and sometimes graph size, changed a bit when the file was saved then reopened. 
  • Sometimes blank preview appeared instead of the graph with changes within Magic Step 2 dialog.
  • The connecting line disappeared starting from the beginning of the gap, if 'When axis is discontinuous, also place gap in line' checkbox was selected.
  • When exporting a graph without a Y axis, extra white space was added above the graph.
  • Parts of Whole graph with exploded slices were cropped (incomplete) on layouts.
  • Pasting data from Excel sometimes lost a column title.
  • If you tried to enter a font name using lower case into the combobox in the toolbar, you got a message, "Could not apply font".
  • Points whose coordinates coincided with an axis limit did not show on the graph when the axes were offset.
  • Error bars were sometimes not shown correctly when the Y axis is logarithmic. The upward pointing error bars were sometimes not shown, when the downward pointing error bar would have gone to a negative value (whcih can't be shown). And the floating alert about downward pointing error bars being impossible sometimes showed even if you only asked for upward pointing error bars. 
  • Prism is limited to 500 sheets per section, but let you dupicate a family which would create more than 500 sheets (but some couldn't be viewed). Now it no longer allows you to creaet more than 500. 

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