Bio-Rad Bio-Plex Data Pro User Manual
Bio-Plex Data Pro™
Software User Guide
Version 1.0
Bio-Plex Data Pro Software User Guide |
BIO-RAD TECHNICAL SUPPORT DEPARTMENT
The Bio-Rad Technical Support Department in the U.S. is open Monday through Friday,
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the Web at www.consult.bio-rad.com.
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Fax: 1-510-741-5802
Email: LSG.TechServ.US@Bio-Rad.com (U.S.)
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NOTICE
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is subject to change without notice. Although prepared to ensure accuracy, Bio-Rad
assumes no liability for errors or omissions, or for any damage resulting from the
application or use of this information.
The following are trademarks of Bio-Rad Laboratories: Bio-Rad, Bio-Plex, Bio-Plex
Manager, and Bio-Plex Data Pro. Luminex, xMAP, and xPONENT are trademarks of
Luminex Corporation. Windows and Excel are trademarks of Microsoft Corporation.
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technology (the “System”) to you, the end-user. By using this System, you agree that (i) the
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this System and by purchasing a kit containing Beads.
Bio-Rad Laboratories, Inc., 2000 Alfred Nobel Drive, Hercules, CA 94547 1-800-424-6723
Copyright © 2001–2011 by Bio-Rad Laboratories. All rights reserved.
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Bio-Plex Data Pro Software User Guide
Table of Contents
Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Basic Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
The Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Toolbar Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Overflow Toolbar Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
File Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Edit Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Data Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
View Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2. Working with Projects . . . . . . . . . . . . . . . . . . . . . . . . 9
Creating a Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Data Sets Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Opening a Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Editing a Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Organizing Your Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Chapter 3. Working With Data Sets . . . . . . . . . . . . . . . . . . . . . 15
Importing Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Importing Data into Bio-Plex Data Pro Software . . . . . . . . . . . . . . . . . 16
Importing Data Directly from Bio-Plex Manager Software . . . . . . . . . . 17
Editing a Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Deleting a Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chapter 4. Organizing the Data . . . . . . . . . . . . . . . . . . . . . . . . . 21
Selecting Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Viewing and Editing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
The Sample Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
About the Sample and Results Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Filtering Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Filtering Data in the Sample and Results Tables . . . . . . . . . . . . . . . . . 24
Filtering Data in the Perform Analysis/Create Charts View . . . . . . . . . 26
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Bio-Plex Data Pro Software User Guide | Table of Contents
Removing Filters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Adding a Column. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Hiding a Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Sorting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Defining a Sort in the Sample or Results Tables . . . . . . . . . . . . . . . . . 30
Clearing Data Sorting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Basic Sorting in Bio-Plex Data Pro Software . . . . . . . . . . . . . . . . . . . . 34
Copying Data in Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Copying a Data Row . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Copying the Data Set Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Viewing Data Values with Full Precision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Copying Plots and Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Exporting Plots and Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Chapter 5. Viewing the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Viewing Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
View Results for All Analytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Merging Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Viewing Merged Data in the Results Table. . . . . . . . . . . . . . . . . . . . . . 42
Viewing Merged Data in the Sample Table . . . . . . . . . . . . . . . . . . . . . 43
Heat Map Result View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Adding a Column. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Chapter 6. Viewing the Results and Basic Statistics . . . . . . . 49
Analysis Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Analysis Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Analysis Configuration Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Analyte Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Interpreting P-Value Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Understanding Fold Change Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Analyte Charts and Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Scatter Plot and Box and Whisker Plot . . . . . . . . . . . . . . . . . . . . . . . . 55
Bar Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Summary Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Export to Statistics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Results by Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Appendix A. Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
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Bio-Plex Data Pro Software User Guide
1 Introduction
Bio-Plex Data Pro™ software provides tools for annotating and analyzing the
results of experiments conducted in Bio-Plex Manager™ software. When you
import Bio-Plex Manager data into Bio-Plex Data Pro, you can edit samples,
view results, and perform statistical analysis on data. These actions take place
within a Bio-Plex Data Pro project.
Basic Workflow
The basic workflow in Bio-Plex Data Pro consists of the following steps:
1. Create a project.
2. Import your data sets (Bio-Plex Results files [.rbx]).
3. Edit your samples.
4. View your results.
5. Analyze your data.
This guide explains how to use Bio-Plex Data Pro to perform the steps in this
workflow.
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Bio-Plex Data Pro Software User Guide | The Workspace
The Workspace
The Bio-Plex Data Pro software Home view displays buttons to create a new
project or to open an existing project. You can also open a recent project by
clicking the project name in the Recent Projects list. The left pane displays the
project workflow, starting at the top with Manage Data Sets and ending with
Perform Analysis/Create Charts. Once a project is open, clicking each button
in the left pane takes you to the view where you complete the step.
Toolbar Commands
Toolbar buttons give you quick access to basic commands. You can also
access these commands from the menus.
Home
New Project
Open Project
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The Workspace
Import Bio-Plex Results File
Undo
Redo
Select Sample Type for analysis
Clear All Analysis Filters
Reset Sample Lists to Default Sort
Merge samples run on different panels/assays
Undo Merge Samples
Overflow Toolbar Commands
Clicking the triangle displays an overflow toolbar of hidden commands.
Overflow toolbars are enabled whenever the screen size does not allow all
toolbar commands to be displayed.
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Bio-Plex Data Pro Software User Guide | The Workspace
Overflow toolbar
Overflow toolbar
File Menu Commands
The following commands can be accessed from the File menu:
• New Project — opens a dialog box in which you specify project
details
• Open Project — opens a dialog box in which you can open an
existing project and organize your projects
• Import Bio-Plex Results File — opens a dialog box, in which you
can browse to a data set and import it
• Exit — closes Data Pro software
Edit Menu Commands
The following commands can be accessed from the Edit menu:
• Undo — removes the effect of an action you performed.
• Redo — restores the effect of an action you undid.
• Cut — copies contents of selected cells to the clipboard and
deletes contents of selected cells that are not read only.
• Copy — copies the contents of selected cells to the clipboard.
• Paste — pastes clipboard contents into the table. Read-only cells
are skipped. When clipboard content is a single value, its content is
copied to each selected cell in the table.
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The Workspace
• Customize Sample Table — opens a dialog box in which you can
select or clear columns or add new columns to the sample table.
• Customize Result Table — opens a dialog box in which you can
hide or display columns, add new columns, and reorder columns.
• Copy Table to Clipboard — copies the entire table to the
clipboard, including the column titles.
• Copy Table to Clipboard Full Precision — copies the data with
full precision to the clipboard.
• Copy Plot to Clipboard — copies selected scatter plot or box and
whisker plot to the clipboard.
• Export Plot — exports plots or graphs to a Portable Network
Graphics (.png), JPEG, bitmap, or TIFF format.
In addition to Edit menu commands, you can use the following commands to
copy, paste, and delete data in tables.
CTRL+A Select All selects the entire table in tables that allow
multiple selections.
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Bio-Plex Data Pro Software User Guide | The Workspace
Copy Table to
Clipboard
CTRL+C Copies the contents of selected cells to the clipboard.
Delete Deletes the content of selected cells if they are not
CTRL+X Copies contents of selected cells to the clipboard and
CTRL+V Pastes clipboard contents into the table. Read-only cells
Right-click the table and select Copy Table to Clipboard
on the context menu to copy the entire table to the
clipboard, including the column titles.
read-only.
deletes content of selected cells that are not read-only.
are skipped. When clipboard content is a single value, its
content is copied to each selected cell in the table.
Data Menu Commands
The following commands can be accessed from the Data menu:
• Select Sample Type for analysis — opens a dialog box in which
you select sample types to use in your analysis. These sample
types are the standards, controls, blanks, and unknowns imported
from Bio-Plex Manager.
• Clear All Analysis Filters — clears all filters in the project.
• Reset Sample Lists to Default Sort — clears all sort settings in
the project.
• Merge samples run on different panels/assays — opens a
dialog box that allows you to merge samples from different data
sets (.rbx files) that share the same identity. Choose the column
that contains the information you need to match samples.
TIP: Use Merge Samples when you notice samples listed several
times that you want analyzed as a single sample.
• Undo Merge Samples — restores the sample row settings.
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The Workspace
View Menu Commands
From the View menu you can access the following:
• Imported data sets in the Data Set Table
• Individual sample data in the Sample Table
• Results in the Results Table (Single Analyte), Multi Analyte Table,
and Heat Map
• Analyze data in Scatter Plot, Box and Whisker Plot, Bar Graph,
Summary Table, Export to Statistics Software table, and Results by
Sample table
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Bio-Plex Data Pro Software User Guide | The Workspace
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Bio-Plex Data Pro Software User Guide
2 Working with Projects
A project is the container for your data. After you create your project, you
import data into the project. You can have as many projects as you like.
Creating a Project
Follow the procedure for creating a new project.
To create a project:
1. From the Home view, click New Project.
The New Project dialog box appears.
Note: You can also create a new project by selecting New Project from
the File menu or clicking New Project in the toolbar.
2. Type a name for the project in the Name box.
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Bio-Plex Data Pro Software User Guide | Creating a Project
3. Type the name of the project owner in the Owner box.
4. (Optional) Type the name of the team.
5. (Optional) Type the name of the supervisor.
6. (Optional) Type a description for the project (up to 255 characters).
7. Click OK.
The Import Bio-Plex Results File dialog box appears.
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Note: The name of the project appears in the Import Into list.
8. Click Browse and navigate to the data sets you want to import.
9. Select the data sets you want to import and click Open.
10. In the Import Bio-Plex Results File dialog box, click Import.
The data sets are copied into the database. When the Status displays
Done, the data sets have been successfully copied.
11. Click Close.
The project opens in the Manage Data Sets view and displays the Data
Sets table.
Data Sets Table
The Data Sets table displays the details for the data sets imported from RBX
files at the plate level. It is most useful immediately after data import, when
you can use it to verify that the imported data are what you want to analyze.
Opening a Project
The following information is displayed for each data set:
Name — displays the name of the data set; by default this is the name of the
imported Bio-Plex Results file (.rbx file).
User Name — displays the name associated with the data set as specified in
the general information page of Bio-Plex Manager.
Acquisition Time — displays the date and time the data were collected on
the Bio-Plex instrument.
Description — displays the data file description entered in the Bio-Plex
Manager RBX file.
Imported Date — displays the date the file was imported into the system.
Imported by — displays the name of the Windows user logged in when
import occurred.
Opening a Project
You can open a project in the Home view by clicking on the project name in
the Recent Projects list or by clicking Open Project.
To open a project:
1. In the Home view, click Open Project.
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Bio-Plex Data Pro Software User Guide | Opening a Project
2. In the Open Project dialog box, click on the project name.
If the project contains data, the project is opened in the Manage Data
Sets view. It displays all the data sets contained in the project. See
Importing Data Sets on page 15 for more information about data sets.
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If the project does not contain data, the Import Bio-Plex Results File
dialog box appears. See Importing Data Sets on page 15 for
information on importing data into your project.
Editing a Project
You can edit project attributes in the Edit project dialog box.
To edit a project:
1. Click Open Project.
The Open Project dialog box appears, displaying a list of projects.
2. Right-click in the row of the project you want to edit, and click Edit Data
Set.
TIP: Do not click the project name; this will open the project.
Editing a Project
The Edit project dialog box appears.
3. Edit the project settings and click OK.
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Bio-Plex Data Pro Software User Guide | Organizing Your Projects
Organizing Your Projects
Over the course of time, you will create multiple projects, and you may not be
working with all of them at the same time. You can organize your projects by
removing projects that you are not currently working on from the list of active
projects and moving them to the Inactive Projects list. You can perform any of
the commands on an inactive project that you perform on an active project;
you can open and edit the project, view the data, and perform statistical
analysis on the data, and so on. You can return inactive projects to the Active
Projects list at any time.
To move a project to the Inactive Projects list:
• From the Active Projects tab in the Open Projects dialog box,
select the project you want to move to the Inactive Projects list and
click Deactivate.
To return a project to the Active Projects list:
• From the Inactive Projects tab in the Open Projects dialog box,
select the project you want to move to the Active Projects list, and
click Activate.
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Bio-Plex Data Pro Software User Guide
3 Working With Data Sets
Bio-Plex Manager™ software results files are imported into Bio-Plex Data
Pro™ software for analysis. You can view the data set in the Manage Data
Sets view. You can also edit the properties of the data set and delete data sets
if you no longer need them for your analysis.
Importing Data Sets
Data are imported into projects from the Import Bio-Plex Results File dialog
box. You can select an existing project or you can create a new project into
which the files are imported.
You control the data that are imported in one of the following ways:
• Add data files using the Import Bio-Plex Results File command.
• From Bio-Plex Manager, import your results directly into Bio-Plex
Data Pro.
All files that appear in the Data Set Files list are imported into the selected
project. You can combine data from multiple experiments into a project. You
can import up to ten data sets (RBX files) into a single Bio-Plex Data Pro
project. Each RBX file represents one data set. You can import data set files
into multiple projects by selecting another project.
The procedure for importing data in Bio-Plex Data Pro differs slightly from
importing through Bio-Plex Manager. See Importing Data into Bio-Plex Data
Pro Software on page 16, and see Importing Data Directly from Bio-Plex
Manager Software on page 17 for more information.
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Bio-Plex Data Pro Software User Guide | Importing Data Sets
Importing Data into Bio-Plex Data Pro Software
The following procedure describes how to import data into Bio-Plex Data Pro.
To import data sets into a project:
1. From Bio-Plex Data Pro, click Import Bio-Plex Results File in
the toolbar.
The Import Bio-Plex Results File dialog box appears.
2. Select the desired project from the Import Into drop-down
list, or create a project by clicking New Project.
3. Click Browse to navigate to and select the data sets you want to import.
4. Click Open.
The Data File field displays the file name, including the path to the file.
The Status displays as Ready.
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5. Click Import.
The system imports all data files in the list. Each file displays a status as
it is imported:
Done — the data set was successfully imported.
Exists — if you try to import a data set that was previously imported
into the project, Bio-Plex Data Pro does not reimport the data. It
displays the status Exists to indicate the data has already been
imported into the project.
Importing Data Sets
Ext. Standards — the data were successfully imported. The unknown
values were calculated using an external standard curve.
Renamed — the data were successfully imported. The name of the file
being imported is the same as a file previously imported into the
project, but the data are different. To distinguish between the two data
sets, the file name of the data being imported is appended with a
number, for example 001 is appended at the end of the file name Bio-
Plex Phosphoprotein 11-Plex 001.
Note: If the data being imported are identical to data previously
imported but they are exported from a different version of BioPlex Manager, Bio-Plex Data Pro imports the data and displays
the Renamed status.
6. You can click Browse and import additional data sets, or click Close if
you are done importing data.
Importing Data Directly from Bio-Plex Manager Software
The Export Results to Bio-Plex Data Pro feature in Bio-Plex Manager allows
you to import data directly into Bio-Plex Data Pro. You initiate the data export
from Bio-Plex Manager. Then the Import Bio-Plex Results File dialog box in
Bio-Plex Data Pro displays automatically. If the Bio-Plex Data Pro program is
not already running, it launches automatically.
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Bio-Plex Data Pro Software User Guide | Editing a Data Set
The Data File field displays the file name and indicates the source as Bio-Plex
Manager. You may import this data set just as you would any RBX file. You can
add more data sets to this list by using the Browse button. You may also
return to Bio-Plex Manager to export another data set.
For more information on this feature, see the Bio-Plex Manager Software 6.1
User Manual.
Editing a Data Set
You can edit the name and description of a data set.
To edit a data set:
1. Open the project whose properties you want to edit.
2. In the Data Sets table, right-click the data set you want to edit, and then
click Edit Data Set in the context menu.
The Edit Dataset dialog box appears.
3. Edit the name and description and click OK.
Deleting a Data Set
The following procedure describes how to delete a data set from your project.
To delete a data set:
1. In the Data Sets table, select the data sets you want to delete.
2. Right-click and select Delete Data Set in the context menu.
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Deleting a Data Set
A message asks you to confirm that you want to delete the data set.
3. Click Yes.
The data sets are deleted from the project.
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