GraphPad Prism 8 User Guide
Contents
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View the Statistics or Regression guide
How to learn Prism
What's new in Prism 8?
What Prism 7 users need to know before using Prism 8
More kinds of graphs
Better looking graphs
Smoother sailing
More efficient
More compatible
More versatile
Multiple regression
Huge improvements in ANOVA
Nested t test and nested one-way ANOVA
More analysis choices: Statistics
More analysis choices: Regression
What was new in earlier versions?
What was new in Prism 7?
Highlights of what was new in Prism 7
What was new: Graphs
Heat maps
Semitransparent colors to see overlapping points
Enter dates or elapsed time as X values
Three way grouped graphs
Improvements with error bars
Other improvements in graphing
What was new: Nonlinear regression
More accurate (asymmetrcial) confidence intervals from nonlinear regression
Test for homoscedasticity
Flag bad fits
More choices for user-defined equations
Improved built-in equatons
What was new: Statistical analyses
Three way ANOVA
Analyze a stack of P values
Control the false discovery rate (FDR)
New analysis to transform concentrations
Choose how to report P values
Improved analyses of 2x2 contingency tables
Other improvements in statistical analyses
What was new: General
Label subcolumns
Color code selected cells in tables
Color code sheet names
New Family menu
New shortcuts to work more efficiently
Uses OS X Versions and Resume (Mac only)
Enter data with more digits
Looks better on high resolution displays
Work with larger files
What was new in Prism 6?
What's new? Highlights
What's new? Statistics
What's new? Multiple comparisons
What's new? Regression
What's new? Time savers
What's new? Data tables
What's new? Working with other programs
What's new? Parts-of-whole data
What's new? Column graphs
What's new? XY Graphs
What's new? Grouped graphs
What's new? Layouts
What was new in Prism 5?
How Prism is unique
Organized data tables
Data analysis for scientists, not statisticians
Everything is hot linked
A complete record of your work
Getting started with GraphPad Prism
A brief tour of Prism
Essential concepts
Welcome dialog
Graph Portfolio
Tutorial Data Sets
The five sections of a Prism project
Adding new sheets to your project
Tips for using Prism
Differences between Windows and Mac versions of Prism
File compatibility between Windows and Mac
Unique to Prism Windows
Features in Windows but not Mac
Working with multiple files in Prism Windows
Automatic back up of Prism files
Unique to Prism Mac
Features in Mac but not Windows
Working with multiple files in Prism Mac
Overview: Resume and Versions in Prism Mac
Details: Resume and Versions in Prism Mac
File..Save As command in Mac
Getting around in Prism
Navigator -- See all sheets in your project
Gallery - View all the sheets of one type
Working with families of sheets
Searching for sheets in a large project
Graph and layout tool tips
Changing the zoom
What if the toolbar or navigator is missing?
Tips for working in a small window
Prism files
Difference between Windows and Mac
PZF vs. PZFX files
File compatibility between Prism versions
Merging and splitting projects
Emailing Prism files to colleagues
LabArchives
Saving vs. exporting
Template, method and example files
Automatic backups of Prism files
Work efficiently. Repeat analyses and graphing
Duplicate a family of sheets
Clone a graph
Use Wand to analyze and graph just like another table
Templates
Template or method (wand)?
Organizing Prism projects
Renaming, sorting, and deleting sheets
Working with multiple sheets at once
Freezing a sheet to prevent changes
Using Info sheets to organize your projects
Annotating your work with floating notes
Color code selected cells in data or results tables
Highlighting sheets in the Navigator tree
Grouping related sheets
Preferences
Tips for navigating large projects
Tips to avoid the need for large projects
Data tables
Distinguishing the eight kinds of data tables
Key concept -- data tables
Prism's eight data table formats
XY tables
Column tables (one grouping variable)
Grouped tables (two grouping variables)
Contingency tables
Stacked vs. side-by-side replicates
Survival tables
Parts of whole tables
Multiple variable tables
Nested tables
The difference between nested and grouped tables
Creating data tables
How to create a new data table
Creating a table to create a bar graph
Creating a table to create a scatter plot
Creating a table to combine bars and points
Inserting a series
Data table limits
Editing data tables
Changing a data table format
Entering dates or elapsed times as X
Column titles
Subcolumn titles
Row titles
Sorting data
Changing data table column widths
Specifying decimal places in a data table
Excluding or highlighting values
Deleting or removing entire data sets
Missing values
Keyboard shortcuts
Rounding
Data objects
Transforming and normalizing?
Importing and exporting data
Linking and embedding data
Changing linked and embedded data
Paste linking data from Prism
Unlinking data objects
Pasting data from Excel (Windows)
Pasting data from Excel (Mac)
Options when pasting data from Excel (win or mac)
Importing data from text files
Importing text and Excel files directly
Importing and pasting choices
Source tab
View tab
Filter tab
Placement tab
Info & Notes tab
Troubleshooting: Negative numbers become positive; fractional numbers become integers?
Exporting from data tables
Analyzing data with Prism
Analyzing data: The basics
What 'analyze' means in Prism
How to analyze data with Prism
Statistical analyses and linear or nonlinear regression
Working with results of analyses
Analysis tabs
Creating chains of analyses
Changing an analysis
Repeating an analysis
Graphing results
Frozen and orphaned analysis results
Excluding data points from an analysis
Embedding results on a graph
Hooking to analysis and info constants
Color coding key results
Transforming, normalizing, etc.
Key concept -- Manipulating data
Transform data
Transforming concentrations
Remove baseline
Normalize
Transpose rows and columns
Prune rows
Fraction of total
Select and transform multiple variable tables
Extract and rearrange from multiple variable tables
Graphs
Creating graphs
New graph of new data
New graph of existing data
Duplicating a graph
Graphs created by analyses
Portfolio graphs
Prism Graphs: the basics
Eight ways to change a graph
Change Graph Type dialog
Changing which data are plotted
The Format Graph dialog
The Format Axes dialog
Prism Magic - Make Graphs Consistent
Rotating, flipping, reversing
Formatting individual symbols and bars
Changing a graph's shape and size
Legends
Graphs with a right Y-axis
Changing fonts on graphs
Bar graphs
Colors
Color schemes
Selecting colors (Mac)
Selecting colors (Windows)
Semitransparent colors
Replicates and error bars
Entering replicates and error values
Key concept -- Replicates and error bars
Entering replicates
Entering error values computed elsewhere
Error bars and confidence bands on Survival graphs
Horizontal error bars
Graphing replicates and error values
Graphing each replicate
Box and whiskers graphs
Violin plots
Graphing error bars computed from replicates
Graphing error bars computed from entered error values
Why do error bars on bar graphs sometimes appear asymmetrical?
Graphing error envelopes
Confidence and prediction bands from regression
The Format Graph Dialog
Overview of Format Graph
How to bring up the Format Graph dialog
Different Format Graph dialogs for different kinds of graphs
Changing one, some or all data sets
Style
Symbol shape and border
Bar borders and fills
Distinguishing the X axis from the bar baseline
Graphing error bars
XY graphs
Format Graph -- XY
Front-to-back order of data sets
Use row titles to label data points
Nudging XY data sets
Skip over some points to speed graphing
Additional XY settings
Adding a line of identity
Point to point lines
Spaghetti plot
Box and whiskers plot
Column graphs
Format Graph --Column
Data set spacing on Column graphs
Plotting order of Column graphs
Additional Column graph settings
Forest plots
Color coding column scatter graphs
Grouped graphs
Appearance of Grouped graphs
Grouped graphs with XY data
Data set grouping and spacing on Grouped graphs
Plotting order of Grouped graphs
Additional Grouped graph settings
Row or column titles under bars?
Plotting the grand mean or grand median
Three way graphs
Contingency graphs
Appearance of Contingency graphs
Data set grouping and spacing on Contingency graphs
Plotting order of Contingency graphs
Additional Grouped graph settings
Row or column titles under bars?
Heat maps
Creating a heat map
Color mapping
Graph settings
Labels
TItles
Gaps
Legend for heat maps
Survival graphs
Appearance of Survival graphs
Changing the plotting order of data sets
Nudging survival data sets
Parts of whole graphs
Changing the look of parts of whole graphs
Changing which data set is plotted
Nested graphs
Appearance tab: Nested graphs
Data sets on graph tab: Nested data
Format Axes dialog
Overview of the Format Axes dialog
Axis range, numbering & titles
Axis range
Axis numbering or titles
Major and minor ticks
Hide an axis and show scale bars
Discontinuous axes
Additional ticks and grids
Axis titles
Labeling axes with dates and times
Elapsed time
Dates
Dates (Compatible with Prism 6)
Logarithmic axes
What is a logarithmic axis?
How to: Create a log axis
Logarithmic axes cannot contain zero or negative numbers
Regression fits the data, not the graph
When to use a logarithmic axis
Advice: Bar graphs with log axes rarely make sense
Graphing logarithms - different than using a log axis
A review of logarithms
Frame and origin
Positioning a graph on the page
Customizing a graph's frame and axes appearance
Showing grid lines
Setting the graph origin
Graphs: Frame and axes
Page layouts
Creating a layout
Placing a graph from the same project on a layout
Placing a graph from another project on a layout
Adding another graph to the layout
Making a graph an unlinked picture
The size of graphs on layouts
Creating a depth chart
Master legends (one legend for several graphs)
Duplicating a layout
Adding text, drawings, results and pictures to graphs or layouts
Adding text
Using Word to add text (Windows only)
Drawing lines, arrows, and shapes
Including pictures and other objects
Tips for moving or rotating objects
Aligning objects on a graph
Adding analaysis results to a graph
Exporting images from Prism
How to export one or more graphs or layouts
Exporting options
The differences between export formats
Exporting for publishing in journals
RGB vs. CMYK color models
Fonts and EPS files
The size of exported graphs and layouts
Clear (transparent) background
Exporting graphs with semitransparent colors
One-click to Microsoft PowerPoint or Word
Embedding or linking Prism graphs in other programs
Printing
Two toolbar buttons for printing
Printing data and results tables
Printing graphs and layouts
Printing the gallery
Custom page size
Scripts
Overview of Prism scripts
Alternatives to scripting
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 example 7. Changing the X-axis title of all graphs
Script details
Script syntax
Navigating a project
How rows and columns are numbered
Adding comments to a script
Loops and simulations
Using variables when outputting text
Creating new sheets
Changing data tables
Changing graphs
Setting the default drive and folder
Opening and saving Prism Files
Importing data from a text file
Importing data from the script file
Copy and paste
Changing info constants
Exporting a graph or layout
Exporting data, results or info tables
Writing to Prism, text, HTML, XML or SQL tables
Writing to text files
The WBlock and WTBlock commands
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
Launching a Prism script from outside Prism (Windows)
Using Prism scripts with Excel
How long can a script be?
Standardizing Prism use in a lab
Locking the preference file
Individual preference files
Shared templates, methods, and examples
Adding your own built-in equations
Using a local LabArchives server
Support and license
Installing Prism
System Requirements
Fire wall settings
Command line switches (Windows only)
Technical support
How to cite GraphPad Prism
GraphPad Prism license agreement
Training
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