GraphPad Prism

5.0

User's Guide

. Getting around in Prism ------------------------------ 4

Prism
. Organizing Prism projects---------------------------- 13
Prism
. Adding to your project--------------------------- 23

Prism files---------------------------------------------32
Prism
Data tables--------------------------------------------39

Error bars and replicates------------------------------68

Importing and exporting data------------------------78

Info sheets--------------------------------------------96

Graphs: the basics-----------------------------------101

2


Graphs: Symbols, bars, lines, and legends-----------114

. Graphs: Frame and axes---------------------------151

Analyzing data with Prism------------------------179

Prism
. Transforming, normalizing, etc. ------------------190

. Page layouts-------------------------------------201

. Adding text, drawings, and pictures to graphs or

layouts------------------------------------------------208

 Getting around in prism

1.
Prism
Prism
Prism

Prism

Prism

ppt
word

2.
Prism

3.Gallery

Gallery

Prism

5.

Ping pong

Ctrl-L

D, R, G

Prism

Prism Data with Results

10

 Data with Results

Prism Preferences View

Prism

6.
11


Zoom Zoom

resize graphs
Zoom
Zoom Out
Ctrl +M

12

Ctrl +J

 Prism

1.
Prism

Prism
F2
Rename sheet

Prism

Edit Reorder
Sheets

Sheet

13

2.

Zoom

14

 Ctrl

Print

Export
word ppt
15

Magic

color scheme
background color or plotting area color
1
23

3.
Prism

Prism

16

4.
Prism
wordppt

Create Link

17

(Windows only)

18

5.

6. Prism Preferences
Prism
19

import export graph

diagnostics

Prism Preference

View
-
-
-
-

File and Printer

-
-Prism5
xml prism pzfx
20

 xml Prism5 Prism4

xml pzfx

-
- prism emfwmf
prism
microsoft office emf wmf

Graph

Analysis

Internet
ftp

Info Sheet

File locations

21

Send to MS Office
word Prism

ppt word

22

1.
Prism

New

data table and graph

new Info sheet new graph of

an existing data table new layout

the
Analyze button.
23


Prism

ClonePrism

Duplicate a family

Open a template

Apply a saved method

2.

Prism

24

Prism

25

Prism Y X

1. Save Special Save as Example

2.
3.
4.

3.

1. New Insert
2. Duplicate Family

26

3.

Prism

VS

Prism

VS

27

4.

Prism

1.
2. Y X
3.

4. Prism Save Special

28

5.
6.

7.

1. Prism
Prism

2.
3.

29

4. Prism

VS

5.

Prism
Method

1. Analyze
2. Method by Example
3.

1.
2. Analyze Data Saved method
3.
30

4.

1. Prism Save Special

Save Method
2.
3.
4.

31

Prism
Prism (PZF )

1.
Prism
Prism

PZF
prism5 prism4
PZFX
xml prism5 XML

Prism
PZFX Prism

PZFX PZXF

Xml
PZFX XSl

32

Prism

vs
prism prism
prism
Export

2. prism
prism
Prism5 prism
Prism4 prism5 PZF
prism4 prism5 PZF prism5

33

Windows
Windows Mac

Mac
windows StuffIt Expander
www.stuffit.co m unstuffing stuffing
), MacBinary BinHex
stuffit expander

prism
windows word ppt prism
prism
prism OLE
prism
prism5 word prism5
prism4 prism4
prism4 prism4 prism5

3. prism

34

 prism
Prism
PZB
prism
prism

prism
Prism
prism File Save Special
Prism CD

prism

PZX PZXF
PZF prism4 prism5
PZFX prism5 pzfx

pzxf prism

prism

35


XML XML
XML

4.
prism
prism

New Merge
Prism
*.

prism
prsim Prism
prism

36

 prism
prism
prism File Save Special Save Family As

Gallery

5. prism

prism Send Send by Email

prism Prism

prism prism5

37


prism png

mapi
mapi

prism
Save
Family As prism Save
Special

Prism
prism prism prism
prism www.graphpad.com
prism

38

Prism

Excel Prism
X Y

1.

Prism
Prism

SD SEM Prism

X X

2. Prism
Prism
Prism

39


XY tables XY XY X Y

Column tables vs vs

vs

Grouped tables

vs vs

Contingency tables
40

Survival tables Prism

Kaplan - Meier log-rank Gehan-Wilcoxon

3.
Prism
Prism

Prism

New
New Data
Table Graph

41

 New

4. XY

XY
XY X Y

XY
-
-
-
-cubic spline and LOESS
-
-

XY

XY

42

XY

43

Prism

X
X 104 Y Y X

44


Prism
Prism

5.

vs

vs vs

T
Mann-Whitney
Wilcoxon

45

 Tukey, Dunnett, Newman-Keuls or Bonferroni post

Kruskal-Wallis
Friedman
Bland-Altman
ROC

Prism

.
Exclude Values.

Prism
46

Mean and
Error

6.
vs
vs

Bonferroni post

47

Prism

VS

VS

Prism

Edit Exclude

values.

X
Y Prism
SD SEM

48

Prism

Prism

Prism

49

7.

():

: .
:

Fishers
Chi-square

50

8.

Prism
Kaplan - Meier log-rank Gehan-Wilcoxon

Prism

Kaplan-Meier

Log-rank

Wilcoxon-Gehan

51

Kaplan - Meier YX

XY

X Prism
Y:
X '1
0
: How To: Survival Analysis
52

9.

XY Prism
SD
SEM
:

Subcolumn Format Change

53


Format Graph

10.

Prism

54

55

XY

X XY

56

11.

Prism

57

XY
XY x
x
XY

XY Format Graph
all to Choose all data setsshow each replicate
Mean and Error

58

Prism

59

Format Graph "One symbol per column"

prism

Format Graph Appearance and Plot drop-down

60

12.

XY

Table format Format

"Show row titles."
x

61


Format Graph "Label each point with its row
title"

62

13.
XY Prism

x
x
Sort Rows

Sort Rows

Change data set order

63

14.

Prism

15.
64


Prism

2 Change decimal format

3 Automatically increase
as needed
prism

16.

65


1
2 Edit Exclude Valueds

prism outlier elimination

Add/Remove data sets

Analyze different data sets

66

17.
prism
Tab

Shift-tab

Enter
Shift-Enter
DEL
prism Edit Delete

Shift-space
Control-space
Control-A

67

Prism

1.

Prism
Prism
Prism
SD SEM Prism
Row Means Prism

2. XY

XY

2 52

68

SD N

"%CV" 100SD/Mean"%CV"Prism SD
N SD, SEM %CV SD, SEM, 95% CI
NPrism

Table Format

69

 Format Data Table SD

SEM
SEM SD
Format Data Table

Prism SD SEM
N SD,SEM 95% CI

Change Type of Graph

Format Graph
all

3.

70

71


all

4.

2 52

grand mean and median

meanSD N

72

Format Data Table SD

SEM
SEM SD
Format Data Table

Prism SD SEM
N SD,SEM 95% CI
73

all

5.

prism
prism SE 95%CILearn more about entering
survival data.

SE XY
prism

(
95%

74


Change graph type

all

6.

Learn more about choosing and graphing prediction and confidence bands from
linear regression and nonlinear regression.

7.

75

 XY

XY
Each Replicate

76

77


1.
Excel text Prism
Prism

Window Mac
Window Excel text
Mac TEXT Excel

2 Excel windows
Prism

Ctrl+V,
Prism Prism

78

Paste Data Prism Excel

Paste Embed

Prism
Prism Excel
Prism
Prism
Paste Link Excel

Excel Prism
Excel Excel

Paste Transpose Excel Prism

Excel Prism Prism

Paste Special windows

Excel Prism
Excel,Prism
Excel

Excel

79

 Excel Prism
Prism Prism

Excel
Windows Excel
Prism

3. Excel MAC
Excel
Prism

80

Paste
Paste Transpose Excel prism
Paste Special Import and Paste Special

Mac Excel
Mac Excel Prism

Excel
Excel Prism
Prism Prism

Excel
Mac prism Excel Excel CSV
Excel CSV

81

4. Text
TXT CSV Prism
Txt Excel
Prism Excel Prism

Excel Text
Excel Txt
CSV

txt CSV

txt csv Prism

Prism

Import and Paste Special

82

 Prism File open TEXT

prism
Import

5. TEXT Excel
Excel Prism
Excel Prism Excel
Prism

Excel XLS Prism WINDOWS

Prism

Import and Paste Special

Excel Excel

Excel
Excel Prism

83

 Excel Prism Excel Excel Excel

Prism Prism Excel Excel
Excel
Excel OLE Prism Excel
Excelprism windows OLE
Mac OLE MAC
Excel.
Excel Prism Prism

Prism
txt
.TXT, .DAT, .CSV, .PRN
ASCII

( ASCII ) Prism
Prism

Import and Paste Special

84

 txt dat

6.

Prism
Prism

Prism

1
Prism

85

Prism Excel

Excel
Excel
Prism
Excel Excel
OLE windows
Prism

Prism Excel
Prism
Prism
Prism
Prism Excel

86

 Prism
Excel Excel

Filter

87


Prism
Prism
99

Excel

88

<=<=>>=<>

Prism

prism

Prism

1
89

Row #

Col. 1

Col. 2

Col. 3

12

123

14

142

13

152

12

116

11

125

15

134

Prism

Row #

First Col.

Second Col.

123

142

152

116

134

125

prism
prism

4
prism
Placement

90


Prism Prism

Prism
Import or Paste Special

Prism Prism
Prism

By rows By columns
30
Prism
91

 A B

1 30 Prism
prism
SD
3 Prism

Prism
Prism

5
Prism
Prism
Prism

92


Prism

7.

P Word PPT
P word PPT

Prism

CSV
CSV comma-delimited values
Preferences dialog

93

Excel Word
Prism CSV X Y

TXT
CSV Tab
Excel Word
Excel Word
Prism TXT X Y

XML
XML
XML

Prism5
Prism5 XML
Prism XML Prism

XML XML
XML

94

 prism XML

Prism XML (prism5xmlschema.xml).

Prism5 XML
XML Prism XML
PZFX

95

 Info sheets
1.
prism
Prism

note

2.

96

 new Insert

prism
Prism
prism preference

automatically create a new Info sheet for every new data

table

97

Import File
prism

7.

98

prism

8.
prism

99

 prism
Prism

100


Prism
Prism

1.

Prism Sheet New

1.
2. New Graph of Existing Data.

3.

101


1.
2. Duplicate Current Sheet

3. type of graph
which data sets are graphed.

1.
2. Duplicate family.

102

3.
4.

1. "New Data Table (+ Graph)".

2. clone

2
Change Graph Type
Change Graph Type

Change Graph Type

103

3.

-Prism

-
Prism

104

Data Sets on Graph

-
-
- Prism change Add/Remove date sets

- Navigator ,
- Remove Data Set or Replace Data Set
105

4. Prism Magic -
Prism Magic
Prism Change Prism Magic
saved

as an example

Prism Magic
1. Prism Gallery
2. Prism Change Magic

3.
Next

4. Prism

106

5. Ok

5.

Format Graph

Format this data point

Format Graph

Frame and Origin

Prism Change
Color Scheme

107

 Prism Prism

Gallery

Color Scheme Define Color Scheme

6.

108

XY
Format this Point

Format this bar.

109


Prism Format graph Format Graph
Graph Settings Remove all individual formatting.

7.

Rotate/Flip Prism Change

110

 XY Survival

Format Graph fine tune that order

Graphs
(aspect ratio)

111

 Prism

x Y

Change Format Axes Frame and Origin

width height
Prism 1.5

1.5
112


Prism Change Resize Graph

More Choices

113

Prism

1. XY
1) XY
Format Graph -XY
change the
look of a single data point
Format Graph

114

Change ALL data sets--. ALL

control
115

SDSEM95%CI range Y

Appearance Plot

Shape
More

116

//

Show Area Fill

Learn more about error bars on XY graphs.

/
117

 VS

-
Prism

front-to-back order

118

 Y
Y Prism

Show legend Label each point with its row title

Revert Legend
to Column Titles

119


Prism Text

2
XY

Prism Change Rotate/Flip

Format Graph Data Sets on Graph

120

Nudging data sets on a graph.

XY row titles
121

 Prism Format graph Format Graph

Label each point with its row title

4 XY

Format Graph Data sets on Graph

X Y
X Y

X Y

122


Y 25

Y 50

Y Y
Y Y

X Y
123

 3D

XY

Format Graph Graph Settings

124

2.
1)
Format Graph

Format Graph

125

Change ALL data sets--. ALL

, SD
SEM95%CI range

126

 A B C D B C

A C B D

//

Learn more about error bars on Column graphs.

127

Y Prism

Show legend
Revert Legend to Column Titles

X
X

128

Prism Format graph Format Graph

Graph Settings

Data Sets on Graph

200
50 0

129

Prism Change Rotate/Flip

Format Graph Data Sets on Graph

130

4
Format Graph Graph Settings
Format Graph Graph Settings

131

Hide Baseline

132


Prism

3.
1

133

 Prism Format graph Format Graph

Graph Settings

Format Graph order

interleaved stacked grouped
superimposed

134

135

Prism Change Rotate/Flip

Format Graph Data Sets on Graph

136

Change Sort Reverse row order

137

See another example of changing plotting order for Grouped graphs.

3
Format Graph Graph Settings
Format Graph Graph Settings

138

X Hide
Baseline

139

dogs

140

4
Format Graph -

Format Graph

141

Change ALL data sets--. ALL

142

,
.

SDSEM95%CI range

143


Data Sets on Graph tab

Learn more about error bars on Grouped graphs.

Y
Y Prism

Show legendPrism

144

Revert Legend to Column Titles

4.
1
Format Graph -

Format Graph

145

Change ALL data sets--. ALL

Shape Prism More

Format Graph
Graph Settings

Learn more about error bars on survival graphs

146

 Format Graph
Graph Settings

All

Y
147

 Y Prism

Show legendPrism

Revert Legend to Column Titles

Prism Change Rotate/Flip

Format Graph Data Sets on Graph

148

Treatment B
Treatment

149

150


Format Axes
Additional Ticks and Grid lines section
Frame and Origin

Format Axes
-

Prism Change Resize Graph

Change
Selected Objects
X
Y Y

Frame Origin

Text

151


1.

1)

Prism Prism Layout

View
Zoom To Fit Page

View Rulers

152

Prism Format Axis Frame and Origin

Prism Arrange Center on page

153

2)

Format Axes Frame and Origin

154

3)

Format Axes Frame and Origin Prism

Format Axis

X Y

X Y

155

Format Axis additional ticks or lines

156

Prism Show Grids View Show

Grids

4)

157

 Prism Format Axis /

Prism Text
Text

text object

158

5)
X Y

Format Axes Frame and Origin Prism

Format Axes

2.

1)

Format Axes Frame and Origin Prism

Format Axis

159


Prism Automatically determine the range and
interval

Prism's Hook

2)

Format Axes Frame and Origin Prism

Format Axis

Format Axes Titles and Fonts Numbering or labeling

Font Font settings

preferences Graph
X Y
Format Axes Titles and Fonds

160


Format Axes (i. e. $) (i. e. %)

90
Format Axes All Ticks

Prism X Y

Y
Enter

DEL

Format Axes Titles and Fonts Show title

Font Format Axes

Font

161

 Text text justify

Format Axes Y

Prism Prism

Format Axes Range Auto Regularly

Spaced Ticks

162

Format Axes Regularly Spaced Ticks

log spacing
4 3

Format Axes All Ticks None for Direction

Format Axes All Ticks

Additional ticks and grid lines.

5 Y
Y
Y X

163

 Format Axes Frame and Origin Prism

Format Axis

Right Y axis

Y
Prism Format Graph Appearance
Right Y axis Y

164

Y :
Prism Y
X Y
Y Y

Prism X Y

165

 Format Axes Frame and Origin Prism

Format Axis

Frame and Origin Show Scale Bars

Format Axes Regularly Spaced Ticks

Format Axes Frames axes

Show Scale Bar
166


DEL

Format Object

Format Object

text T

Format Axes Regularly Spaced

Ticks

1. Format Axes Gaps and Directions

167

2.

3.

X Format Axes Gaps and Direction Two segments

0-15 67% 15-50

33%

168

X 0 0 X=-9
-9.5 -8.5 12%
-8.5 2.5 88%

0-24 50% 48-72,

50%

Format Axes Additional Ticks and Grid Lines

169

Format Axes Additional Ticks and Grid Lines Details

170


Prism

Format Axes Additional Ticks and Grid Lines

Details Format Additional Ticks and Grid lines Delete Ticks

171

 analysis constant info

constant Additional Ticks and Grid lines Details Format
Additional Ticks and Grids Hook

Kd BMax Kd BMax
172

3.

X
100nM X
10

1
10 1000.
1000 3 10
e2.7183
173

X Y

X Y=+*X
X X

Y
174

3
Prism Y

4 4 4
Y

Y 0.001, 10, 100.

175

Y Prism

Y
Format Axes
Format Bars Graph Settings

Format Axes Scale Log10 Log 2.

10 100 20, 30, 40, 50, 60, 70,

80 90
9

176


Format Axes Numbering or Labeling
Prism
10, 100, 1000, 10000, etc.
1101 , 1102 , 1103, 1104,, etc.
10 101 , 102 , 103, 104,, etc.
1, 2, 3, 4, etc.

Format Axes Numbering or Labeling

Equal or Log

177


Analyze Transforms X = log(X).
Create a New Graph of the resultsPrism
Analyze

10

178

. Prism
Prism

1. Prism
Prism analyze
Prism analyze

. Analyze
1. Analyze

Prism
2. Built-in analysis.

3.
179


4. Prism

. Analysis parameters

Learn

.
Prism Results

Prism Interpret Analysis checklist

180

2.

Prism

Preference View Data + Results

Results
Analysis Parameters
181

---
---

4.

Prism Prism
embedded
hooked

Prism
orphaned

Sheet

182

5.

Change Exclude

See also:
Excluding data table values from graphs and analyses

6.

Prism

183


etc

Prism's Text

184

7.

Prism

Analysis

Nonlinear regression

Values that can be hooked

Best-fit value of each parameter
Lower confidence limit of each parameter
Upper confidence limit of each parameter

Survival analysis

Bland-Altman

Median survival
Bias
Lower 95% confidence limit of bias
Upper 95% confidence limit of bias

Column statistics

Mean with lower and upper confidence limits

Geometric mean with lower and upper
confidence limits
Lowest value
Highest value
QC control lines (Mean plus or minus 1, 2 or 3

185

SD)
SD
SEM
N
Sum

1. QC

186

Hook

- Y Format Axes Y
details

Format Additional Ticks and Grids Y

hook QC
187


Format Additional Ticks and Grids
QC

2. EC50

EC50 95% Additional

ticks and grid lines

188

189

.
1.

Prism

+
Data+Results
Prism excel
Prism Prism excel
excel excel

2.

190

 Y X

Y= Y * K
Y=Y+K
Y=YK
Y=Y/K
Y = Y squared
Y=Y^K
10
Y = log(Y)
Y = -1*log(Y)
( e)
Y = ln(Y)
10 Yth ().
Y = 10 ^ Y
eY ()
Y = exp(Y)
Y = 1/Y

Y = sqrt(Y)
ln(Y/1-Y)
Y = logit(y)
Y 0.0 1.0
Y = probit(Y)
Y 1
Y = rank(Y)
.
Y = zscore(Y)
Y .
191

Y = sin(Y)
Y = cos(Y)
Y = tan(Y)

Y = arcsin(Y)

Y = ABS(Y)

. =0. =K

Y = Y+Random
Y=X/Y
Y=Y/X
Y=YX
Y=Y+X
Y=Y*X
Y=XY
K K Y
K K K
K K

X Y
X Y X Y
XY
-Prism Y X
192


- Y SD SEM, Prism Y X
XYY
- X Y Prism XY X
Y Y X

Y Prism
SEM
NPrism

95%
95%

3.

Eadie-Hofstee, Hanes-Woolf Lineweaver-Burk

Scatchard Hill

193

Eadie-Hofstee

Y/X

Hanes-Woolf

X/Y

Hill

log()

log10(Y/(Ym
ax-Y))

.
(Prism
Log10(X)

Ymax)

Lineweaver-Burk

1/X

1/Y

Log-log

Log10(X)

Log10(Y)

Scatchard

Y/X

Prism Bland-Altman plots

separate analysis

4.
X Y

194


<B>
B<~A> A

- Y X X Y
X Y Prism X
A Prism B
A
-if-then Prism if
If if if
NOT AND OR

MAX>100
Ymax=Constraint
(A<B or A<C)
195

NOT(A<B AND A<C)

FRACTION<>1.0
X<=A and X>=B
<><=>=

Y= IF (Y<Y0, Y, Y*Y)
Y Y0 Y Y Y
Y Y
0.

5.

- Analyze built-in analyses

196

-Prism
Y X
X
Prism

6.
Y
EC50
0% 100%
S
Prism
197

 Analyze Built-in analyses

Normalize

0% 100% 0
100
Prism

-0% 100%

-X
- SEM
- 0.000
1.000

198

7.
Y
104 Prism
104

8.

199

 Analyze Built-in analyses

Prune

200

.
1.

Prism
- PPT
- Prism
-
-
-

2.
New Insert

201

 New Layout

Prism

3.

202

203

4.

-
- Prism
- Prism
tab

204


1.

-
-
2.
Prism
- Prism
Prism
-

-
100%

5.

-
CTRL

-
205

Prism
ALT

Prism

206

1.

2. 3

3.

Prism

207

.
1
Prism

Prism
Wingdings

Prism

208

Prism
15

209

Alt

2. Word
word Windows
word Prism Word Prism
-- Word
Prism
Word
word

Prism Word Word

word word
210

 Prism word
Prism word word /
excel excel
Prism

3.

1.

Prism
2.
3. control
shift

211

4.

Prism
OLE Prism Prism

Object linking and embedding

SmartDraw Windows

SmartDraw SmartDraw
SmartDraw SmartDraw
www.smartdraw.com

212

 Prism Windows

Prism
Prism ok

Windows Prism bmpjpgpcx

png tiff Mac Prism bmpjpgpictpng tiff
windows wmf Mac pict
Prism

Prism

5.

Prism
213

shift

shift
shift

ctrl

ALT Prism

214

6.

Prism
Prism
ALT

215

 Prism

X Y

216

Ctrl M J

217

Prism 0.1 1

218