GraphPad Prism is a powerful combination of basic biostatistics, curve fitting and scientific graphing in one comprehensive program.

Tutorial - Analyzing Dose-Response Data

Follow a step-by-step to transform and normalize the data, and fit a curve with nonlinear regression.

GraphPad Prism 6.0

GraphPad Library

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.

What makes Prism truly unique, however, is not just what it does, but how it does it. Designed for laboratory and clinical researchers, Prism doesn't expect you to be a statistician. It guides you through the analysis process – giving you as much help as you need – and tracks and organises your work like no other program available. You can concentrate on your data, not on figuring out how to use the program.

Curve Fitting

Nonlinear regression fits a model to your data. You pick a model that corresponds to the experimental design from Prism's a menu of the 15 equations biologists use most, including those that describe dose-response curves, one- and two-site binding and competition, and one-and two-phase exponential association and decay. You can also enter your own equation.

Prism then automatically analyses an entire family of data sets at once. You don’t need to repeat any commands. Prism automatically creates the graph with curve, error bars and legend – ready to customise. The results are stores with your data and graphs, along with your analysis choices so you can inspect your choices and results at any time and add notes to explain what you did and what you concluded. When you repeat an experiment, simply replace the data, and Prism repeats all the analyses and redraws the graphs. You can instantly set up a template to analyse and graph your routine experiments, with no programming or macros.

Statistics

Prism makes it very easy to perform basic statistical tests commonly used by laboratory researchers and clinicians. It does not take the place of the big statistics programs, however it offers a complete set of statistical analyses up to two-way ANOVA, including analysis of contingency tables and survival curves. Prism does not perform ANOVA higher than two-way, or multiple, logistic or proportional hazards regression.

Experiment Organisation

With Prism you can store all parts of an experiment (several data tables linked to results, graphs, page layouts and notes) in one organised file. You can decide how much information to include in one project file. You can place all your data tables into one file, along with linked results and graphs. Or you can also separate your work into lots of files. Prism lets you choose how to organise your work.

Features of GraphPad Prism

Curve fitting

  • Marquardt-Levenberg nonlinear regression.

  • Fit data to a built-in classic equation, choose from an equation library, or enter your own.

  • Built-in equations include kinetic equations (exponential decay, growth, association), equilibrium mass action equations (binding isotherm, sigmoidal dose-response, competitive binding including 2 site), polynomial up to 4th order, Gaussian distribution, power series and sine.

  • Enter multiple-line user-defined equations, including If-Then clauses. Define different equations for different data sets (columns).

  • Generate a family of theoretical curves.

  • Create equation libraries to distribute to others.

  • Fit data to two equations and compare fits with an F test. Automatically graph the best fit.

  • Fit several data sets at once, sharing selected parameters between the data sets.

  • Compare two curves by comparing the sum of squares when selected parameters are shared between the data sets with the individual sum of squares.

  • Compare models (and data sets) using the extra sum-of-squares F test or Akaike's Information Criterion (AIC).

Data management

  • Enter Y data as raw replicates or mean, SD/SEM and N.

  • Automatic updating of analyses and graphs as data change.

  • Enter up to 104 related data sets on one table to be analyzed and plotted together. Up to 52 replicates and any number of points per data set

  • Accurately accounts for missing values.

  • Exclude specified points from analyses and graphs (they show on the table in blue italics, but are ignored by the analyses and graphs).

  • Transfer data to and from Excel and other applications with the clipboard, or import and export text (ASCII) files.

  • Import text files and retain the link. Double click on the Prism data to edit the text file.

  • Choose rows and columns to import.

  • Filter row. Choose to start importing after a condition is met, and to stop importing when another condition is met.

  • Filter columns. Choose a range of columns to import.

  • Decimate. Skip several rows after every row that is imported.

  • Unstack indexed data.

  • Transpose rows and columns.

  • Import free-form notes and structured info constants along with data.

  • Copy and paste data and results between Prism and Excel.

  • Paste a link from Excel into Prism. Double-click on the Prism data to return to Excel (Windows only).

  • Embed an entire spreadsheet file within a Prism file (Windows only).

  • Import Excel files directly (Windows only).

  • Normalise, sort or transpose data.

  • Subtract (or divide by) a baseline or compute relative changes.

  • Consolidate related data sets by calculating means or totals.

  • Transform data with a full range of mathematical functions, including user-defined transforms.

  • Smooth curves, or convert to their derivative or integral.

Statistics

  • Calculate slope and intercept with confidence intervals.

  • Force regression lines 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.

  • Determine new points along the standard curve.

  • Pearson or Spearman (nonparametric) correlation.

  • Table of XY coordinates.

  • Calculate min, max, quartiles, mean, SD, SEM, CI, CV, Geometric mean with Confidence Intervals.

  • Specify desired level of confidence.

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

  • Kolgoromov-Smirnov normality test.

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

  • Skewness and Kurtosis.

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

  • Paired or unpaired t tests.

  • Mann-Whitney or Wilcoxon tests.

  • Ordinary or repeated measures one-way ANOVA with Tukey, Newman-Keuls, Dunnett or Bonferroni post tests, or the post-test for trend.

  • 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.

  • Repeated measures two-way ANOVA with some post tests.

  • Bland-Altman plots.

  • Receiver operator characteristic (ROC) curves.

  • Deming regression (type ll linear regression).

Graphing

  • Linear, log10, or log2 scale, ascending or descending numbering.

  • Segment axes with up to two breaks (gaps) per axis.

  • Select orientation of tick marks and adjust major and minor intervals. Choose tick length.

  • Label ticks using decimal, scientific, 10^X, or notation.

  • Place custom ticks and labels anywhere on an axis.

  • Offset X and Y axes.

  • Add a right-hand Y axis.

  • Choose number of decimal points for axis numbering.

  • Precede axis numbers with a prefix (i.e. "$") and follow with a suffix (i.e. "%")

  • Numbering under X axis can be at any angle.

  • Move numbering and axis title closer to, or further from, the axis.

  • XY graphs, bar graphs (vertical or horizontal), box-and-whisker plots, and scatter plots.

  • Plot hundreds data sets on a single graph. Add or remove data sets.

  • Create graphs with no frame, a plain frame, a frame with ticks, or a frame with a grid.

  • Adjust size and shape of graph by specifying dimensions or dragging with the mouse.

  • 14 different symbols in 9 sizes.

  • 5 line patterns (dotted, dashed, etc.) in 7 line thicknesses and 16 colors.

  • Connect points with a line, staircase, or spline curve.

  • Start point-to-point lines at the origin or the first data point.

  • Change origin position: lower left, automatically selected, or custom.

  • Built-in drawing tools--lines, arrows, boxes, circles, ovals, and arcs.

  • Automatic calculation of error bars from replicate values.

  • Plot mean and SD, mean and SEM, mean and 95% CI, mean and range, median and range, or median and interquartile range.

  • Error bars can be above or below the point, or both, and with caps or without.

  • Specify error bar thickness.

  • Option to suppress error bars.

  • Automatic legends that are customisable.

  • Easily access Greek letters, mathematical symbols, or international characters.

  • Rotate text any angle.

  • Add underlining, bold, super and subscripts, or change point size easily from the tool bar.

  • Move graph and axis titles without losing centering.

Page layout

  • Built-in page layout templates for automatic arrangement of multiple graphs.

  • Move, resize, delete or add graphs.

  • Include data, results tables and graphs on one page.

  • Import images as .TIF, .PCX, .BMP, .JPG .GIF, .WMF (Windows) or PICT (Mac) files.

  • Create portrait and landscape pages in one file.

  • Tools to equalize the size, and align axes, of several graphs.

  • 6 levels of zoom.

  • Layouts will automatically update when you edit a graph or data plotted on the graph – even if the graph comes from a different Prism file.

  • Draw lines, arrows, boxes, circles, ovals and arcs.

  • Add text, including Greek letters and super- or subscripts.

  • Align objects (left, right, center, top, bottom) or align graphs by X or Y axes.

  • Send to back. Bring to front.

  • Duplicate objects or groups of objects.

  • Group and ungroup objects.

  • Use rulers, snap to guidelines, superimpose grid.

  • Choose any color for any data set or object, and define your own palette of custom colors.

  • Embed OLE objects, such as equations and WordArt. (Windows only)

  • Paste any portion of a data, results or info table onto a graph or layout.

  • Customize the table with a border, grid lines, or titles.

  • Create text tables as well as numerical tables.

  • Place any number of tables on one graph or layout page.

  • Prism automatically updates tables when you edit the data.

  • Print in color or black and white.

  • Copy and paste into Word or PowerPoint.

  • One-click copy and paste into a new slide in PowerPoint (Windows only).

  • Embed or link a Prism graph into PowerPoint or Word using OLE (Windows only).

  • Export as a wmf (Windows) or pict (Mac) file.

  • Export as a bitmap in png, bmp, jpg, or tif format at up to 1200 dots per inch.

  • Choose RGB or CMYK colors. Choose whether to include background color in exported file.

  • Email an entire file, or just one page, right from Prism (Windows only).

  • Post one graph or layout, or all graphs or layouts, to a web server.

Windows and Mac Differences

The main difference is that the Mac version does not support Object Linking and Embedding (OLE):

  • When you copy and paste a graph created with Prism Windows into another program such as Word or PowerPoint, you can embed an entire Prism object or paste a link to the Prism file. You can then double-click on the graph from within Word or PowerPoint to edit the graph with Prism. Since the Mac OS does not support Object Linking and Embedding (OLE), you can only paste a picture of a Prism graph into another program. Double-clicking on the pasted graph does not launch Prism.

  • Prism Windows can embed objects (for example, equations) created by other programs. You double-click on an object to edit with the program that created it. Prismfor Macintosh, however, does not support Object Linking and Embedding (OLE). With Prism Mac, you can copy and paste pictures from another program, but you need to go back to the original file in order to edit with the other program.

  • When you paste Excel data, Prism Windows can embed the entire workbook within Prism, or maintain a link between Prism and the Excel file. With Prism Mac, you simply paste the values from Excel. Prism Mac cannot maintain a link to the Excel file.

  • With Prism Windows, you can press one button to send a graph (or layout) to PowerPoint or Word. We were not able to build these buttons into the Mac version, so instead you need to the steps sequentially: copy the graph to the clipboard, switch to PowerPoint, insert a new slide, and paste. However you can send to Keynote with one click.


Resources

Fitting Models to Biological Data Using Linear and Nonlinear Regression

PDF version of the text book: Fitting Models to Biological Data Using Linear and Nonlinear Regression. The printed version is included when you buy GraphPad Prism.

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