| -----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 |
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