| -----GRAPHPAD PRISM 5 ----- |
 | A tour of Prism |
 | Tour overview |
| 1. Start a new project |
| 2. Enter or import data |
| 3. Automatic graphing |
| 4. Analyze your data |
| 5. Customize your graph |
| 6. Print or export |
| 7. Repeating work by cloning |
| 8. Change a graph to match another |
| 9. Combine graphs in a layout |
| 10. Automatic linking and updating |
| 11. Adding notes and other helpful tools |
| Getting started |
| Tips for using Prism |
| Guided examples: Statistical analyses |
| Guided examples: Nonlinear regression |
| ----- PRISM 5 USERS GUIDE----- |
| Getting around in Prism |
| Key concept -- Five sections |
| Navigator -- See all sheets in your project |
| Gallery - View all the sheets of one type |
| Follow graph and layout tool tips |
| Tools for navigating large projects |
| Changing the zoom |
| Organizing Prism projects |
| Renaming, sorting, and deleting sheets |
| Working with multiple sheets at once |
| Freezing a sheet to prevent changes |
| Annotating your work with floating and audio notes |
| Highlighting sheets in the Navigator tree |
| Default preferences |
| Adding to your project |
| Creating new sheets |
| Clone a graph |
| Duplicate a family |
| Open a template |
| Apply a saved method |
| Prism files |
| Saving - file formats and compression |
| File compatibility between Prism versions |
| Backing up Prism files |
| Merging and splitting projects |
| Emailing Prism files to colleagues |
| Data tables |
| Key concept -- data tables |
| Prism's five data table formats |
| How to create a new data table |
| About XY data tables |
| About Column (one grouping variable) tables |
| About Grouped tables (two-grouping variables) |
| About Contingency tables |
| About Survival tables |
| Changing a data table format |
| Which table should I use to create a bar graph? |
| Which table should I use to create a scatter plot? |
| Row titles |
| Sorting data |
| How to change data table column widths |
| Specifying decimal places in a data table |
| Excluding data table values from graphs and analyses |
| Keyboard shortcuts |
| Error bars and replicates |
| Key concept -- Replicates and error bars |
| Replicates and error bars on XY graphs |
| Replicates and error bars on Column graphs |
| Replicates and error bars on Grouped graphs |
| Error bars and confidence bands on Survival graphs |
| Confidence and prediction bands from regression |
| Graphing each replicate |
| Importing and exporting data |
| Key concept -- linking and embedding data |
| Pasting data from Excel (Windows) |
| Pasting data from Excel (Mac) |
| Importing data from text files |
| Importing text and Excel files directly |
| Importing and pasting options |
| Source |
| View |
| Filter |
| Placement |
| Info & Notes |
| Changing linked and embedded data |
| Exporting from data tables |
| Info sheets |
| Key concept -- what is an Info Sheet? |
| Creating and formatting Info sheets |
| Hooking Info constants |
| Placing Info constants on graphs or layouts |
| Graphs: the basics |
| Creating graphs |
| Changing the type of graph |
| Changing which data are plotted |
| Prism Magic - Make Graphs Consistent |
| Colors and color schemes |
| Formatting individual symbols and bars |
| Rotating, flipping, reversing |
| Setting a graph's shape and size |
| Graphs: Symbols, bars, lines, and legends |
| XY graphs: Formatting symbols and lines |
| Appearance of XY graphs |
| Front-to-back order of data sets |
| Use row titles to label data points |
| Nudging XY data sets |
| Additional XY settings |
| Column graphs: Bar formatting and spacing |
| Appearance of Column graphs |
| Data set spacing on Column graphs |
| Plotting order of Column graphs |
| Additional Column graph settings |
| Grouped (& contingency) graphs: Symbols and line formatting |
| Data set grouping and spacing on Grouped graphs |
| Plotting order of Grouped graphs |
| Additional Grouped graph settings |
| Appearance of Grouped and Contingency graphs |
| Survival graphs: Formatting options |
| Appearance of Survival graphs |
| Changing the plotting order of data sets |
| Nudging survival data sets |
| Graphs: Frame and axes |
| Frame, grid and titles |
| Positioning a graph on the page |
| Customizing a graph's frame and axes appearance |
| Showing grid lines |
| Show, hide, or modify titles |
| Setting the graph origin |
| Axes |
| Axis range |
| Axis numbering |
| Axis titles |
| Major and minor ticks |
| Graphs with two Y-axes |
| Hide an axis and show scale bars |
| Put a gap in an axis |
| Additional ticks and grids |
| Logarithmic axes |
| A review of logarithms |
| Making an axis logarithmic does not change the data |
| Advice: Bar graphs with log axes rarely make sense |
| Create a log axis and set numbering and ticks |
| Transform data to logs and graph the results |
| Analyzing data with Prism |
| How to analyze data with Prism |
| Creating chains of analyses |
| Changing an analysis |
| Updating and freezing analysis results |
| Excluding data points from an analysis |
| Embedding results on a graph |
| Hooking to analysis constants |
| Transforming, normalizing, etc. |
| Key concept -- Manipulating data |
| Standard transforms |
| Transforms for pharmacology and biochemistry |
| User-defined transforms |
| Remove baseline |
| Normalize |
| Transpose rows and columns |
| Prune rows |
| Page layouts |
| Key concept -- what is a layout? |
| Creating layouts |
| Choosing a basic arrangement |
| Adding graphs to layouts |
| Aligning and sizing graphs on a layout |
| Master legends |
| Adding text, drawings, and pictures to graphs or layouts |
| Adding text |
| Using Word to add text |
| Drawing lines, arrows, and shapes |
| Including pictures and other objects |
| Tips for moving pictures around |
| Aligning objects on a graph |
| Exporting images from Prism |
| How to export one or more graphs or layouts |
| One-click to Microsoft PowerPoint or Word (Windows only) |
| Embedding or linking Prism graphs in other programs |
| Copy and paste with Macs |
| Posting graphs to a Web site |
| Printing |
| Two toolbar buttons for printing |
| Printing Prism tables |
| Printing graphs and layouts |
| Print preference settings |
| For power users |
| Scripts |
| Key concept -- What is a Prism script? |
| Example scripts |
| Script example 1. Repeatedly import data |
| Script example 2. Monte Carlo analysis |
| Script example 3. Import several files onto one table |
| Script example 4. Open a template and import data |
| Script example 5. Import data and info constants from the script file |
| Script example 6. Import data into several tables |
| Script syntax |
| General commands |
| Adding comments to a script |
| Loops and simulations |
| Creating new sheets |
| Changing data tables |
| Changing graphs |
| Setting the default drive and folder |
| Opening and saving Prism Files |
| Importing data |
| Changing info constants |
| Including data and info constants in the script file |
| Exporting a graph or layout |
| Exporting data, results or info tables |
| Copy and paste |
| Writing to Prism, text, HTML, XML or SQL tables |
| Writing to text files |
| Send to Microsoft Office |
| Special purpose commands |
| Running a Prism script |
| Creating and running a script from Prism |
| Run a script using Automator, MacScript, or AppleScript |
| Launch a script from an intranet web page |
| Launching a Prism script from outside Prism (Windows) |
| Using Prism scripts with Excel |
| Sharing Prism in a lab |
| File locations for templates, methods, and example files |
| Customizing sample scripts |
| Adding your own equations |
| Using Prism on a network |
| Installing Prism on a network |
| Testing networking with a demo |
| Support and license |
| Technical support |
| How to cite Prism |
| License agreement |
| Annual site licenses |
| Training |
| ----- PRISM 5 STATISTICS GUIDE ----- |
| Statistical principles |
| The big picture |
| When do you need statistical calculations? |
| Extrapolating from 'sample' to 'population' |
| Why statistics can be hard to learn |
| The need for independent samples |
| Ordinal, interval and ratio variables |
| The Gaussian Distribution |
| Importance of the Gaussian distribution |
| Origin of the Gaussian distribution |
| The Central Limit Theorem of statistics |
| Standard Deviation and Standard Error of the Mean |
| Key concepts: SD |
| Computing the SD |
| How accurately does a SD quantify scatter? |
| Key concepts: SEM |
| Computing the SEM |
| The SD and SEM are not the same |
| Advice: When to plot SD vs. SEM |
| Confidence intervals |
| Key concepts: Confidence interval of a mean |
| Interpreting a confidence interval of a mean |
| Other confidence intervals |
| Advice: Emphasize confidence intervals over P values |
| One sided confidence intervals |
| P Values |
| What is a P value? |
| Common misinterpretation of a P value |
| One-tail vs. two-tail P values |
| Advice: Use two-tailed P values |
| Advice: How to interpret a small P value |
| Advice: How to interpret a large P value |
| Hypothesis testing and statistical significance |
| Statistical hypothesis testing |
| Extremely significant? |
| Advice: Avoid the concept of 'statistical significance' when possible |
| A Bayesian perspective on interpreting statistical significance |
| A legal analogy: Guilty or not guilty? |
| Advice: Don't keep adding subjects until you hit 'significance'. |
| Statistical power |
| Key concepts: Statistical Power |
| An analogy to understand statistical power |
| Type I, II (and III) errors |
| Using power to evaluate 'not significant' results |
| Advice: Don't compute the power to detect the difference actually observed |
| Advice: How to get more power |
| Multiple comparisons |
| Key concepts: multiple comparisons |
| Approaches to dealing with multiple comparisons |
| Testing for equivalence |
| Key concepts: Equivalence |
| Testing for equivalence with confidence intervals or P values |
| Outliers |
| What is an outlier? |
| Advice: Beware of identifying outliers manually |
| Detecting outliers with Grubbs’ test |
| Statistical tests that are robust to the presence of outliers |
| Dealting with outliers in Prism |
| Nonparametric tests |
| Key concepts: Nonparametric tests |
| Advice: Don't automate the decision to use a nonparametric test |
| The power of nonparametric tests |
| Nonparametric tests with small and large samples |
| Advice: When to choose a nonparametric test |
| Descriptive statistics and normality tests |
| Column statistics |
 | How to: Column statistics |
 | Analysis checklist: Column statistics |
| Interpreting results: Mean, geometric mean and median |
| Interpreting results: Quartiles and the interquartile range |
| Interpreting results: Variance and coefficient of variation (CV) |
| Interpreting results: Skewness and kurtosis |
| Interpreting results: Normality test |
| Interpreting results: One-sample t test |
| Interpreting results: Wilcoxon signed rank test |
| Frequency Distributions |
| Visualizing scatter and testing for normality without a frequency distribution |
| How to: Frequency distribution |
| Graphing tips: Frequency distributions |
| Fitting a Gaussian distribution to a frequency distribution |
| Describing curves |
| Smoothing, differentiating and integrating curves |
| Area under the curve |
| Row statistics |
| Overview: Side-by-side replicates |
| Row means and totals |
| Comparing two groups (t tests ...) |
| Key concepts: t tests and related nonparametric tests |
| Q&A: Entering t test data |
| Choosing a t test |
| Q&A: Choosing a test to compare two groups |
| Unpaired t test |
| How to: Unpaired t test from raw data |
| How to: Unpaired t test from averaged data |
| Interpreting results: Unpaired t |
| Graphing tips: Unpaired t |
| Advice: Don't pay much attention to whether error bars overlap |
| Analysis checklist: Unpaired t test |
| Paired t test |
| How to: Paired t test |
| Testing if pairs follow a Gaussian distribution |
| Interpreting results: Paired t |
| Graphing tips: Paired t |
 | An alternative to paired t test: Ratio t test |
| Analysis checklist: Paired t test |
| Mann-Whitney test |
| How to: Mann-Whitney test |
| Interpreting results: Mann-Whitney test |
| The Mann-Whitney test doesn't really compare medians |
| Analysis checklist: Mann-Whitney test |
| Wilcoxon matched pairs test |
| How to: Wilcoxon matched pairs test |
| Results: Wilcoxon matched pairs test |
| Analysis checklist: Wilcoxon matched pairs test |
| Comparing three or more groups (one-way ANOVA ...) |
| Key concepts: One-way ANOVA |
| Choosing a one-way ANOVA |
| Q&A: Entering one-way ANOVA data |
| Q&A: One-way ANOVA |
| One-way ANOVA |
| How to: One-way ANOVA |
| Interpreting results: One-way ANOVA |
| Analysis checklist: One-way ANOVA |
| Repeated-measures one-way ANOVA |
| How to: Repeated measures one-way ANOVA |
| Interpreting results: Repeated measures one-way ANOVA |
| Analysis checklist: Repeated-measures one way ANOVA |
| Kruskal-Wallis test |
| How to: Kruskal-Wallis test |
| Interpreting results: Kruskal-Wallis test |
| Analysis checklist: Kruskal-Wallis test |
| Friedman's test |
| How to: Friedman test |
| Interpreting results: Friedman test |
| Analysis checklist: Friedman's test |
| Multiple comparison tests |
| Key concepts: Multiple comparison tests |
| Advice: Choosing a multiple comparisons test |
| Post test for trend |
| Planned comparisons |
| Other multiple comparison tests |
| Q&A: Multiple comparisons tests |
| Two-way ANOVA |
| Key concepts: Two-way ANOVA |
| Entering two-way ANOVA data |
| Choosing two-way ANOVA |
| Point of confusion: ANOVA with a quantitative factor |
| Q&A: Two-way ANOVA |
| Ordinary (not repeated measures) two-way ANOVA |
| How to: Two-way ANOVA |
| Interpreting results: Two-way ANOVA |
| Graphing tips: Two-way ANOVA |
| How Prism computes two-way ANOVA |
| Analysis checklist: Two-way ANOVA |
| Repeated measures two-way ANOVA |
| What is repeated measures? |
| How to: Two-way ANOVA. Repeated measures by row |
| How to: Two-way ANOVA. Repeated measures by column |
| Graphing tips: Repeated measures two-way ANOVA |
| Interpreting results: Repeated measures two-way ANOVA |
| Analysis checklist: Repeated measures two-way ANOVA |
| Post tests after two-way ANOVA |
| What post tests can Prism perform following two-way ANOVA? |
| How Prism calculates post tests after two-way ANOVA |
| Calculating more general post tests |
| Categorical outcomes |
| The Confidence Interval of a proportion |
| An example of the confidence interval of a proportion |
| How to compute the 95% CI of a proportion |
| The meaning of “95% confidence” when the numerator is zero |
| A shortcut equation for a confidence interval when the numerator equals zero |
| Contingency tables |
| Key concepts: Contingency tables |
| How to: Contingency table analysis |
| Fisher's test or chi-square test? |
| Interpreting results: Relative risk and odds ratio |
| Interpreting results: Sensitivity and specificity |
| Interpreting results: P values from contingency tables |
| Analysis checklist: Contingency tables |
| Graphing tips: Contingency tables |
| Survival analysis |
| Key concepts. Survival curves |
| How to: Survival analysis |
| Q & A: Entering survival data |
| Example of survival data from a clinical study |
| Example of survival data from an animal study |
| Analysis choices for survival analysis |
| Interpreting results: Kaplan-Meier curves |
| Interpreting results: Comparing two survival curves |
| Interpreting results: Comparing >2 survival curves |
| Multiple comparisons of survival curves |
| Analysis checklist: Survival analysis |
| Graphing tips: Survival curves |
| Diagnostic lab analyses |
| ROC Curves |
| Key concepts: Receiver-operator characteristic (ROC) curves |
| How to: ROC curve |
| Interpreting results: ROC curves |
| Analysis checklist: ROC curves |
| Comparing Methods with a Bland-Altman Plot |
| How to: Bland-Altman plot |
| Interpreting results: Bland-Altman |
| Analysis checklist: Bland-Altman results |
| ----- PRISM 5 REGRESSION GUIDE ----- |
| Correlation |
| Key concepts: Correlation |
| How to: Correlation |
| Interpreting results: Correlation |
| Analysis checklist. Correlation |
| Fitting a curve without a model |
| Spline and Lowess curves |
| Using nonlinear regression with an empirical model |
| Generating curves and simulating data |
| Plotting a function |
| Simulating data with random error |
| Using a script to simulate many data sets |
| Simulations and script to assess confidence intervals |
| Linear regression |
| Key concepts: Linear regression |
| The goal of linear regression |
| How linear regression works |
| Advice: Avoid Scatchard, Lineweaver-Burke and similar transforms |
| Advice: When to fit a line with nonlinear regression |
| How to: Linear regression |
| Finding the best-fit slope and intercept |
| Interpolating from a linear standard curve |
| Results of linear regression |
| Slope and intercept |
| r2, a measure of goodness-of-fit of linear regression |
| Is the slope significantly different than zero? |
| Comparing slopes and intercepts |
| Runs test following linear regression |
| Analysis checklist: Linear regression |
| Graphing tips: Linear regression |
| Deming regression |
| Key concepts: Deming regression |
| How to: Deming regression |
| Analysis checklist: Deming regression |
| Nonlinear regression |
| Key concepts in nonlinear regression |
| Introducing nonlinear regression |
| The goal of nonlinear regression |
| The differences between linear and nonlinear regression |
| Distinguishing nonlinear regression from other kinds of regression |
| Preparing data for nonlinear regression |
| Understanding models |
| What is a model? |
| Three example models |
| Why can't GraphPad Prism choose a model? |
| Advice: How to understand a model |
| Comparing models |
| Questions that can be answered by comparing models |
| Approaches to comparing models |
| How the F test works to compare models |
| How the AICc computations work |
| Global nonlinear regression |
| What is global nonlinear regression? |
| Using global regression to fit incomplete datasets |
| Fitting models where the parameters are defined by multiple data sets |
| Column constants |
| Advice: Don't use global regression if datasets use different units |
| Outlier elimination and robust nonlinear regression |
| When to use automatic outlier removal |
| When to avoid automatic outlier removal |
| Outliers aren't always 'bad' points |
| The ROUT method of identifying outliers |
| Robust nonlinear regression |
| How nonlinear regression works |
| Why minimize the sum-of-squares? |
| How nonlinear regression works |
| Unequal weighting in nonlinear regression |
| How standard errors and confidence intervals are computed |
| How confidence and prediction bands are computed |
| Replicates |
| How dependency is calculated |
| Nonlinear regression tutorials |
| Example: Fitting an enzyme kinetics curve |
| Example: Comparing two enzyme kinetics models |
| Example: Interpolating from a sigmoidal standard curve |
| Example: Automatic outlier elimination (exponential decay) |
| Example: Global nonlinear regression (dose-response curves) |
| Example: Ambiguous fit (dose-response) |
| Nonlinear regression with Prism |
| Choosing a built-in model |
| Dose-response - Key concepts |
| What are dose-response curves? |
| The EC50 |
| Confidence intervals of the EC50 |
| Hill slope |
| Choosing a dose-response equation |
| Converting concentration to log(concentration) |
| Dose-response - Stimulation |
| Equation: log(agonist) vs. response |
| Equation: log(agonist) vs. response -- Variable slope |
| Equation: log(agonist) vs. normalized response |
| Equation: log(agonist) vs. normalized response -- Variable slope |
| Dose-response - Inhibition |
| Equation: log(inhibitor) vs. response |
| Equation: log(inhibitor) vs. response -- Variable slope |
| Equation: log(inhibitor) vs. normalized response |
| Equation: log(inhibitor) vs. normalized response -- Variable slope |
| Dose-response -- Special |
| Asymmetrical (five parameter) |
| Equation: Biphasic dose-response |
| Equation: Bell-shaped dose-response |
| Equation: Operational model - Depletion |
| Equation: Operational model - Partial agonist |
| Equation: Gaddum/Schild EC50 shift |
| Equation: EC50 shift |
| Equation: Allosteric EC50 shift |
| Equation: ECanything |
| Receptor binding - Key concepts |
| Law of mass action |
| Nonspecific binding |
| Ligand depletion |
| The radioactivity web calculator |
| Receptor binding - Saturation binding |
| Key concepts: Saturation binding |
| Equation: One site -- Total binding |
| Equation: One site -- Fit total and nonspecific binding |
| Equation: One site -- Total, accounting for ligand depletion |
| Equation: One site -- Specific binding |
| Equation: One site -- Specific binding with Hill slope |
| Equation: Two sites -- Specific binding only |
| Equation: Two sites -- Fit total and nonspecific binding |
| Equation: One site with allosteric modulator |
| Receptor binding - Competitive binding |
| Key concepts: Competitive binding |
| Equation: One site - Fit Ki |
| Equation: One site - Fit logIC50 |
| Equation: Two sites - Fit Ki |
| Equation: Two sites - Fit logIC50 |
| Equation: One site - Ligand depletion |
| Equation: One site - Homologous |
| Equation: Allosteric modulator |
| Receptor binding - Kinetics |
| Key concepts: Kinetics of binding |
| Equation: Dissociation kinetics |
| Equation: Association kinetics (one ligand concentration) |
| Equation: Association kinetics (two ligand concentrations) |
| Equation: Association then dissociation |
| Equation: Kinetics of competitive binding |
| Enzyme kinetics |
| Key concepts: Terminology |
| Key concepts: Assumptions |
| Key concepts: Choosing a model |
| Equation: Michaelis-Menten model |
| Equation: Determine kcat |
| Equation: Allosteric sigmoidal |
| Equation: Competitive inhibition |
| Equation: Noncompetitive inhibition |
| Equation: Uncompetitive inhibition |
| Equation: Mixed-model inhibition |
| Equation: Substrate inhibition |
| Equation: Tight inhibition (Morrison equation) |
| Exponential |
| Key concepts: Exponential equations |
| Key concepts: Derivation of exponential decay |
| Equation: One phase decay |
| Equation: Plateau followed by one phase decay |
| Equation: Two phase decay |
| Equation: Three phase decay |
| Equation: One phase association |
| Equation: Plateau followed by one phase association |
| Equation: Two phase association |
| Equation: Exponential growth |
| Lines |
| Key concepts: Fitting lines |
| Equation: Fitting a straight line with nonlinear regression |
| Equation: Segmental linear regression |
| Equation: Fitting a straight line on a semi-log or log-log graph |
| Equation: Fitting a straight line on a graph with a probability axis |
| Polynomial |
| Key concepts: Polynomial |
| Equations:: Polynomial models |
| Gaussian |
| Key concepts: Gaussian |
| Equation: Gaussian distribution |
| Equation:: Log Gaussian distribution |
| Equation: Cumulative Gaussian distribution |
| Equation: Lorentzian |
| Sine waves |
| Standard sine wave |
| Damped sine wave |
| Sinc wave |
| Classic equations from prior versions of Prism |
| Equation: One site binding (hyperbola) |
| Equation:Two site binding |
| Equation: Sigmoidal dose-response |
| Equation: Sigmoidal dose-response (variable slope) |
| Equation: One site competition |
| Equation: Two site competition |
| Equation: Boltzmann sigmoid |
| Equation: One phase exponential decay |
| Equation: Two phase exponential decay |
| Equation: One phase exponential association |
| Equation: Two phase exponential association |
| Equation: Exponential growth |
| Equation: Power series |
| Equation: Sine wave |
| Equation: Gaussian distribution |
| Writing your own model (equation) |
| How to: Enter a new equation |
| How to: Clone an equation |
| How to: Manage your list of equations |
| Limitations when entering equations |
| Syntax of user-defined equations |
| Available functions for user-defined equations |
| Fitting different segments of the data to different models |
| Fitting different data sets to different equations |
| Rules for initial values |
| Default constraints |
| Transforms to report |
| Nonlinear regression choices |
| Which choices are essential? |
| Fit tab |
| Compare tab |
| Constrain tab |
| Weights tab |
| Initial values tab |
| Range tab |
| Output tab |
| Diagnostics tab |
| Nonlinear regression results |
| Interpreting results: Nonlinear regression |
| Standard errors and confidence intervals of parameters |
| Normality tests of residuals |
| Goodness of fit of nonlinear regression |
| Runs test |
| Replicates test |
| Dependency and covariance matrix |
| Could the fit be a local minimum? |
| Outliers |
| Why results in Prism 5 can differ from Prism 4 |
| Interpreting results: Comparing models |
| Interpreting comparison of models |
| Interpreting the extra sum-of-squares F test |
| Interpreting AIC model comparison |
| How Prism compares models when outliers are eliminated |
| Analysis checklists: Nonlinear regression |
| Analysis checklist: Fitting a model |
| Analysis checklist: Comparing nonlinear fits |
| Analysis checklist: Interpolating from a standard curve |
| "Bad initial values" |
| "Interrupted" |
| "Not converged" |
| "Ambiguous" |
| "Hit constraint" |
| "Don't fit" |
| "Too few points" |
| "Perfect fit" |
| "Impossible weights" |
| Graphing nonlinear regression |
| How to: Graphing nonlinear regression curves |
| Confidence and prediction bands |
| Residual plot |
| Graphing outliers |