GraphPad Prism

Analyze, graph and present scientific data faster than ever with Prism 7

Overview

GraphPad Prism, available for both Windows and Mac computers,  combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization.

 GraphPad Prism was originally designed for experimental biologists in medical schools and drug companies, especially those in pharmacology and physiology. Prism is now used much more broadly by all kinds of biologists, as well as social and physical scientists.  More than 200,000 scientists in over 110 countries rely on Prism to analyze, graph and present their scientific data. It is also widely used by undergraduate and graduate students.

Nonlinear regression

Nonlinear regression is an important tool in analyzing data, but is often more difficult than it needs to be. No other program simplifies curve fitting like Prism. In fact, you can usually fit curves in a single step. Just select an equation from the extensive list of commonly used equations (or enter your own equation) and Prism does the rest automatically -- fits the curve, displays the results as a table, draws the curve on the graph, and interpolates unknown values.

 Place data for multiple data sets side-by-side on an organized data table, and Prism can fit them all the data sets at once. You can fit the same model separately to each data set, use global nonlinear regression to share parameter values among data sets, or fit different models to different data sets.

 Don't be fooled by the simplicity. Prism also gives you many advanced fitting options. It can report the confidence intervals of the best-fit parameters as asymmetrical ranges (profile likelihood method), which are far more accurate than the usual symmetrical intervals.  It can also automatically interpolate unknown values from a standard curve (i.e., to analyze RIA data), compare the fits of two equations using an F test or Akaike's Information Criterion (AIC), plot residuals, identify outliers, differentially weight data points, test residuals for normality, and much more.

Understandable statistics

While it won't replace a heavy-duty statistics program, Prism lets you easily perform basic statistical tests commonly used by laboratory and clinical researchers. Prism offers t tests, nonparametric comparisons, one-,  two- and three-way ANOVA, analysis of contingency tables, and survival analysis. Analysis choices are presented in clear language that avoids unnecessary statistical jargon.

Unlike other programs, Prism provides understandable statistical help when you need it. Press "Learn" from any data analysis dialog and Prism's online documentation will explain the principles of the analysis to help you make appropriate choices. Once you've made your choices, Prism presents the results on organized, easy-to-follow tables. The Prism documentation goes beyond anything you would expect. More than half of it is devoted to thorough explanations of basic statistics and nonlinear curve fitting, to teach you what you need to know to appropriately analyze your data.

Analysis checklists

Once you’ve completed the analysis, Prism’s unique analysis checklists help you make sure you chose an analysis appropriate for your experimental design, and that you understand the assumptions behind the analysis.

Retrace every analysis

It isn’t really science unless you can document exactly how your data were analyzed. WIth Prism this isn’t a problem. You’ll never wonder how the results got there. Even if the work was done by someone else, you can review (and change) all analysis choices, and see the sequence of analyses (i.e. that the X values were transformed to logarithms before the curve was fit). Similarly, you can easily check if error bars represent the SD or SEM (or something else).

Automation without programming

All parts of your Prism project are linked. This means that when you fix a data entry error, Prism automatically updates all results, graphs, and layouts. Another advantage is that you can instantly analyze a repeat experiment. After you’ve polished the analysis and graphing steps with data from one experiment, you don’t have to repeat all those steps. Prism provides several ways to recycle your work -- to instantly analyze and graph a repeat experiment, without repeating any tedious steps and without requiring any scripting or programming. Prism also offers a scripting language for those who want more complex automation.

Automatic error bars

If you enter raw data, Prism can automatically plot error bars as SD, SEM, range,  interquartile range, or 95% confidence interval.

If you computed error values elsewhere, enter them into labeled (SD or SEM) subcolumns. Prism’s analyses (i.e. t test, ANOVA, regression) will take into account the SD (or SEM) and sample size.

A complete record of your work

A Prism project file can contain more than data, analyses and graphs. A Prism file can be a complete record of your experiments. Each file can contain any number of data tables, info pages, analysis results, graphs, and page layouts.

Data tables can contain not only the data you analyze and graph, but also the data you decided to exclude, which remain on the data table (in blue italics). You can highlight values you want to review later.

Each info page can store both unstructured notes and structured info constants such as lot numbers, concentrations, notebook page numbers, etc.

Graphs and layouts can be embellished with text, lines, arrows, boxes, tables, equations, pictures and more.

Annotate any page with color-coded floating notes, and highlight (in a color you choose) the names of pages you want to look at again, or want someone else to review.

Save Prism files on your computer or network, or save directly to LabArchives, a cloud-based laboratory notebook.

Ready to publish

Prism takes you from raw data to a graph (or layout) ready for presentations, posters or publications. A single click sends completed graphs or layouts to PowerPoint or Word. Copy and paste works too, of course. Export to TIFF, EPS, JPG, or PDF (and more), with all the options you need to satisfy the requirements of scientific journals.

What's new in Prism 7?

Prism 7 lets you do more kinds of statistical analyses, make more kinds of graphs, and organize your data with more flexibility.

Here are some of the highlights.

Heat maps  

Three-way ANOVA

FDR approach to multiple comparisons

More accurate (asymmetrical, likelihood) confidence intervals from nonlinear regression

Label subcolumns  

 

Color code sheet names, and selected cells in tables

Semitransparent colors so you can see overlap

Enter dates (or elapsed times) as X values

Statistical comparisons

•Paired or unpaired t tests. Reports P values and confidence intervals.

•Nonparametric Mann-Whitney test, including confidence interval of difference of medians.

•Kolmogorov-Smirnov test to compare two groups.

•Wilcoxon test with confidence interval of median.

•Perform many t tests at once, using False Discover Rate (or Bonferroni multiple comparisons) to choose which comparisons are discoveries to study further.

•Ordinary or repeated measures one-way ANOVA followed by the Tukey, Newman-Keuls, Dunnett, Bonferroni or Holm-Sidak multiple comparison tests, the post-test for trend, or Fisher’s Least Significant tests.

•Many multiple comparisons test are accompanied by confidence intervals and multiplicity adjusted P values.

•Greenhouse-Geisser correction so repeated measures one-way ANOVA does not have to assume sphericity. When this is chosen, multiple comparison tests also do not assume sphericity.

•Kruskal-Wallis or Friedman nonparametric one-way ANOVA with Dunn's post test.

•Fisher's exact test or the chi-square test. Calculate the relative risk and odds ratio with confidence intervals.

•Two-way ANOVA, even with missing values with some post tests.

•Two-way ANOVA, with repeated measures in one or both factors. Tukey, Newman-Keuls, Dunnett, Bonferron, Holm-Sidak, or Fishers LSD multiple comparisons testing main and simple effects.

•Three-way ANOVA (limited to two levels in two of the factors, and any number of levels in the third).

•Kaplan-Meier survival analysis. Compare curves with the log-rank test (including test for trend).

Column statistics

•Calculate min, max, quartiles, mean, SD, SEM, CI, CV,

•Mean or geometric mean with confidence intervals.

•Frequency distributions (bin to histogram), including cumulative histograms.

•Normality testing by three methods.

•One sample t test or Wilcoxon test to compare the column mean (or median) with a theoretical value.

•Skewness and Kurtosis.

•Identify outliers using Grubbs or ROUT method.

Linear regression and correlation

•Calculate slope and intercept with confidence intervals.

•Force the regression line through a specified point.

•Fit to replicate Y values or mean Y.

•Test for departure from linearity with a runs test.

•Calculate and graph residuals.

•Compare slopes and intercepts of two or more regression lines.

•Interpolate new points along the standard curve.

•Pearson or Spearman (nonparametric) correlation.

•Analyze a stack of P values, using Bonferroni multiple comparisons or the FDR approach to identify "significant" findings or discoveries.

Nonlinear regression

•Fit one of our 105 built-in equations, or enter your own.

•Enter differential or implicit equations.

•Enter different equations for different data sets.

•Global nonlinear regression – share parameters between data sets.

•Robust nonlinear regression.

•Automatic outlier identification or elimination.

•Compare models using extra sum-of-squares F test or AICc.

•Compare parameters between data sets.

•Apply constraints.

•Differentially weight points by several methods and assess how well your weighting method worked.

•Accept automatic initial estimated values or enter your own.

•Automatically graph curve over specified range of X values.

•Quantify precision of fits with SE or CI of parameters. Confidence intervals can be symmetrical (as is traditional) or asymmetrical (which is more accurate).

•Quantify symmetry of imprecision with Hougaard’s skewness.

•Plot confidence or prediction bands.

•Test normality of residuals.

•Runs or replicates test of adequacy of model.

•Report the covariance matrix or set of dependencies.

•Easily interpolate points from the best fit curve.

Clinical (diagnostic) lab statistics

•Bland-Altman plots.

•Receiver operator characteristic (ROC) curves.

•Deming regression (type ll linear regression).

Simulations

•Simulate XY, Column or Contingency tables.

•Repeat analyses of simulated data as a Monte-Carlo analysis.

•Plot functions from equations you select or enter and parameter values you choose.

Other calculations

•Area under the curve, with confidence interval.

•Transform data.

•Normalize.

•Identify outliers.

•Normality tests.

•Transpose tables.

•Subtract baseline (and combine columns).

•Compute each value as a fraction of its row, column or grand total.

System requirements

•Prism 7 for Windows runs under either the 32- or 64-bit versions of Windows Vista, 7, 8 or 10.  Prism will run in a screen as small as 800 x 540. While it runs fine on 64 bit versions of Windows, it is a 32 bit program.

•Prism 7 for Macintosh requires OS X 10.9 (Mavericks) or later.

•Prism requires 90 megabytes of space on the hard drive.

GraphPad Prism's official website: http://www.graphpad-prism.cn/