Site Map

• Improved Outcomes: Home - Software for gene expression (microarray) and proteomics analysis as well as software conulting for bioinformatics, image guided surgery (IGS) and information technology (IT).
• Improved Outcomes: About Us - Background of the company and its founders.
• Improved Outcomes: Contact - For software sales for gene expression (microarray) and proteomics analysis, support, as well as software consulting for bioinformatics, image guided surgery (IGS) and information technology (IT).
• Improved Outcomes: Products - GeneLinker software for gene expression (microarray) and proteomics analysis.
• Improved Outcomes: Products - GeneLinker Feature List for Gene Expression (microarray) and proteomics data analysis.
• Improved Outcomes: Sales - Online ordering GeneLinker software for gene expression (microarray) and proteomics analysis.
• Improved Outcomes: Download - GeneLinker Software for gene expression (microarray) and proteomics analysis.
• Installation Procedure
• Upgrading GeneLinker(TM) Gold
• Uninstallation Procedure
• Updating Demo License to License Server
• Upgrading GeneLinker(TM) Platinum
• Uninstallation Procedure
• License Overview
• Updating Demo License to License Server
• Updating Demo License to Licensed Client
• Starting the Program
• Exiting the Program
• Saving
• GeneLinker(TM) Database
• Setting Up a DB2 GeneLinker(TM) Database
• Setting Up an Oracle GeneLinker(TM) Database
• Contact Information for Predictive Patterns Software Inc.
• Changing from Licensed Client to License Server
• Licensed Client: Configuration Change
• Licensed Client: Moving From One Computer to Another
• License Server: Moving from One Computer to Another
• License Server: Configuration Change
• Updating Floating Client after Server Move
• Improved Outcomes, Software for Life, Kingston, Ontario
• Improved Outcomes: Services - Data Analysis for Gene Expression (microarray) and proteomics.
• Improved Outcomes: Documents on gene expression (microarray) and proteomics analysis.
• Front Page
• Contact Information for Predictive Patterns Software Inc.
• GeneLinker(TM) Tour - Introduction
• Reliability Measures
• Importing Multiple Files With One Sample Each
• Importing Data from Affymetrix MAS 4.0 Files
• Importing Data from Affymetrix MAS 5.0 Files
• Creating a Table View of Reliability Data
• Removing Values by Reliability Measure
• Variables Overview
• Importing Variables
• Overview of ANOVA
• Gene List Filtering (Subsetting)
• Performing an ANOVA
• ANOVA Viewer
• Logarithm
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• Variable Manager
• Variable Viewer
• Confusion Matrix
• Creating Variables
• Sample Removal
• Generating Reports
• Generating Reports
• Datasets Overview
• Using the Experiments Navigator
• The Navigator
• Using the Genes Navigator
• Using the Gene Lists Navigator
• Renaming a Dataset or Experiment
• The Navigator
• Using the Genes Navigator
• Using the Gene Lists Navigator
• The Description Pane
• Viewing Experiment Parameters
• The Navigator
• Using the Genes Navigator
• Using the Gene Lists Navigator
• The Description Pane
• Two-Color Data
• Importing Data from GenePix Files
• Importing Data from Quantarray Files
• Importing Data from ScanArray Files
• Creating an Intensity-Bias Plot of a Sample Ratio
• Lowess
• Subtraction of Central Tendency
• Overview of Lowess Normalization
• Lowess
• Subtraction of Central Tendency
• GeneLinker(TM) Tour - Main Window Layout
• GeneLinker(TM) Tour - Clustering and PCA
• GeneLinker(TM) Tour - Platinum SLAM Classification
• GeneLinker(TM) Tour - Platinum IBIS Classification
• GeneLinker(TM) Tour - Common Functions
• GeneLinker(TM) Tour - Conclusion
• Main Program Functions List
• Shared Selection
• Creating a Table View of Gene Expression Data
• Creating a Color Matrix Plot
• Annotations Overview
• Annotations Viewer/Editor
• Exporting an Image
• Creating a Summary Statistics Chart
• Normalization Overview
• Linear Regression
• Division by Central Tendency (Mean)
• Division by Central Tendency (Median)
• Positive and Negative Control Genes
• Lowess
• Subtraction of Central Tendency
• Logarithm
• Subtraction of Central Tendency
• Lowess
• Divide by Maximum
• Scaling Between 0 and 1
• Standardize
• Filtering Overview
• Replacing Missing Values with an Arbitrary Value
• Maximum Culling
• Range Culling
• N-Fold Culling with N
• Range Culling
• Spotted Array N-Fold Culling
• Spotted Array N-Fold Culling
• Gene List Filtering (Subsetting)
• Performing an ANOVA
• ANOVA Viewer
• Generating Reports
• Agglomerative Hierarchical Clustering Overview
• Exporting Data
• Exporting to DecisionSite
• Exporting a Gene List
• GeneLinker(TM) Gene List Native File Format
• Exporting to PathwayAssist
• Exporting a Gene List
• GeneLinker(TM) Gene List Native File Format
• Overview of Estimating Missing Values
• Replacing Missing Values with an Arbitrary Value
• Nearest Neighbors Missing Value Estimation
• Estimating Missing Values by a Measure of Central Tendency
• Removing Values by Expression Value
• Gene Lists Overview
• Gene List Filtering (Subsetting)
• Importing a Gene List
• Conflict Resolution
• Exporting a Gene List
• GeneLinker(TM) Gene List Native File Format
• Modifying or Deleting Gene Lists
• How to Import Expression Data
• Importing Multiple Files With One Sample Each
• Importing Data from GenePix Files
• Importing Data from Quantarray Files
• Importing Data from ScanArray Files
• ANN Classification and Prediction Overview
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• Creating a SOM Plot
• Annotations Viewer/Editor
• Customizing the SOM Plot
• Resizing the SOM Plot
• Color By Gene Lists or Variables
• Creating a Color Matrix Plot
• Color Manager
• Creating a Two Way Matrix Tree Plot
• Creating a Matrix Tree Plot
• Changing the Gradient Color and Scale
• Resizing Cells in a Color Grid
• Toggling the Color Grid On or Off
• Profile Matching
• Creating a Color Matrix Plot
• Creating a Two Way Matrix Tree Plot
• Creating a 3D Score Plot
• 3D Plot Functions
• Variables Overview
• Importing Variables
• Overview of ANOVA
• Gene List Filtering (Subsetting)
• Performing an ANOVA
• ANOVA Viewer
• Logarithm
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• Variable Manager
• Variable Viewer
• Confusion Matrix
• Creating Variables
• Sample Removal
• Generating Reports
• Classification Plot Classification Results
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• Variable Manager
• Overview of Principal Component Analysis (PCA) Functionality
• Performing PCA for a Dataset
• Creating a Loadings Color Matrix Plot
• Creating a Scree Plot
• Creating a Loadings Line Plot
• Creating a Loadings Scatter Plot
• Creating a Score Plot
• IBIS Overview
• IBIS Search Results Viewer
• Create IBIS Classifier From IBIS Search Results
• Create IBIS Classifier Using a Gene or Gene Pair
• Genes Overview
• Annotations Viewer/Editor
• SLAM(TM) Association Viewer
• IBIS Search
• IBIS Search Results Viewer
• Create IBIS Classifier From IBIS Search Results
• Create IBIS Classifier Using a Gene or Gene Pair
• Tutorial 7: Appendix: Minimum Standard Deviation in IBIS
• Tutorial 7: Conclusion
• Tutorial 7: Step 8 Display IBIS Gradient Plot
• Tutorial 7: Step 7 View IBIS 2D LDA Search Results
• Classifier Gradient Plot
• Color Manager
• Creating a Two Way Matrix Tree Plot
• SVM Classification and Prediction Overview
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• Troubleshooting
• List of System Messages
• Handling a System Crash or Hang
• General Formatting Conventions
• Improved Outcomes, Software for Life, Kingston, Ontario
• Tutorial/Use Case Scenarios
• Tutorial 1: Introduction
• Tutorial 1: Step 1 Start GeneLinker(TM) and Import the Data
• GeneLinker(TM) Tour - Main Window Layout
• GeneLinker(TM) Tour - Clustering and PCA
• GeneLinker(TM) Tour - Platinum SLAM Classification
• GeneLinker(TM) Tour - Platinum IBIS Classification
• GeneLinker(TM) Tour - Common Functions
• GeneLinker(TM) Tour - Conclusion
• Tutorial 1: Step 2 View and Normalize the Data
• Table Viewer Functions
• Creating a Scatter Plot
• Tutorial 1: Step 3 View Parameters and Rename Experiment
• Tutorial 1: Step 4 Perform Hierarchical Clustering
• Tutorial 1: Step 5 Create a Matrix Tree Plot
• Tutorial 1: Step 4 Perform Hierarchical Clustering
• Tutorial 2: Introduction
• Tutorial 2: Conclusion
• Tutorial 2: Figure 1 - Clustering of the cancer cell lines according to gene expression profiles
• Generating Reports
• Generating Reports
• Tutorial 2: Step 10 Generate Report and Export Image
• Tutorial 1: Step 7 Create a Centroid Plot
• Tutorial 1: Step 6 Perform Partitional Clustering
• Tutorial 1: Step 5 Create a Matrix Tree Plot
• Tutorial 1: Step 4 Perform Hierarchical Clustering
• Tutorial 1: Step 8 Create a Cluster Plot
• Tutorial 1: Step 9 Generate Report and Export Image
• Tutorial 1: Conclusion
• Tutorial 2: Step 9 Color Samples by Class
• Tutorial 2: Step 8 Import Cancer Class Variable
• Tutorial 2: Step 7 Create a Matrix Tree Plot
• Tutorial 2: Step 6 Perform Hierarchical Clustering
• Tutorial 2: Step 1 Start GeneLinker(TM) and Import the Data
• Tutorial 2: Step 2 Estimate Missing Data Values
• Tutorial 2: Step 3 Rename the Dataset
• Tutorial 2: Step 4 Display Color Matrix Plots
• Tutorial 2: Step 5 Import a Gene List
• Tutorial 2: Step 6 Perform Hierarchical Clustering
• Tutorial 3: Introduction
• Jarvis-Patrick Clustering Overview
• Distance Metrics Overview
• Euclidean and Euclidean Squared Distance Metrics
• Manhattan Distance Metric
• Chebychev Distance Metric
• Spearman Rank Correlation Distance Metric
• Glossary of Terms/Acronym List
• Disclaimer
• GeneLinker(TM) Product Suite
• GeneLinker(TM) Feature List
• Performing Jarvis-Patrick Clustering
• Clustering Overview
• Creating a Centroid Plot
• Creating a Cluster Plot
• Selecting Items
• Creating a Coordinate Plot
• Changing the Gradient Color and Scale
• Resizing Cells in a Color Grid
• Toggling the Color Grid On or Off
• Displaying an Expression Value
• Shared Selection
• Creating a Table View of Gene Expression Data
• Creating a Color Matrix Plot
• Lookup Gene
• Find
• Find Next
• Find Previous
• Find Previous
• Find Next
• Disclaimer
• GeneLinker(TM) Product Suite
• GeneLinker(TM) Feature List
• Affymetrix Identifiers
• GenBank Identifiers
• UniGene Identifiers
• Annotations Overview
• Annotations Viewer/Editor
• Creating a Gene List Within GeneLinker(TM)
• Importing a Gene List
• Conflict Resolution
• Exporting an Image
• Configuring Plot Components
• Resizing a Plot
• Creating a Summary Statistics Chart
• Tutorial 3A: Step 1 Normalize the Data
• Tutorial 3A: Step 2 Perform Partitional Clustering
• Tutorial 3A: Step 3 Create a Matrix Tree Plot
• Tutorial 3B: Step 1 Estimate Missing Values
• Tutorial 3B: Step 2 Perform Partitional Clustering
• Tutorial 3B: Step 3 Create a Matrix Tree Plot
• Tutorial 3: Conclusion
• Tutorial 4: Introduction
• Overview of Self-Organizing Maps (SOMs)
• Performing a SOM Experiment
• Creating a SOM Centroid Plot
• Creating a SOM Cluster Plot
• Creating a SOM Matrix Tree Plot
• Creating a SOM Plot
• Annotations Viewer/Editor
• Customizing the SOM Plot
• Resizing the SOM Plot
• K-Means Clustering Overview
• Distance Metrics Overview
• Euclidean and Euclidean Squared Distance Metrics
• Manhattan Distance Metric
• Chebychev Distance Metric
• Spearman Rank Correlation Distance Metric
• Glossary of Terms/Acronym List
• Disclaimer
• GeneLinker(TM) Product Suite
• GeneLinker(TM) Feature List
• Clustering Overview
• Pearson Correlation and Pearson Squared Distance Metric
• Tutorial 4: Step 1 Import the Data
• Tutorial 4: Step 2 View the Data
• Tutorial 4: Step 3 Display Summary Statistics
• Tutorial 4: Step 4 Remove Negative Values
• Tutorial 4: Step 5 Remove Genes that have Missing Values
• Tutorial 4: Step 6 Normalize the Data
• Tutorial 4: Step 7 Display Summary Statistics
• Tutorial 4: Step 8 Create a SOM Experiment
• Tutorial 4: Step 9 Create a SOM Plot
• Tutorial 4: Conclusion
• Tutorial 5: Introduction
• Tutorial 5: Step 1 Import the Data
• Tutorial 5: Step 2 Principal Component Analysis
• Tutorial 5: Step 3 Display a Scree Plot
• Tutorial 5: Step 4 Display a Loadings Line Plot
• Tutorial 5: Step 5 Display a Loadings Color Matrix Plot
• Tutorial 5: Step 6 Display a Score Plot
• Tutorial 5: Step 7 Display a 3D Score Plot
• Tutorial 5: Conclusion
• Sample Workflow Using Spotted Array N-Fold Culling With Log Transformation
• Importing One File Containing All Samples
• Selecting a Template for Data Import
• Importing Multiple Files With One Sample Each
• Importing Data from Affymetrix MAS 4.0 Files
• Importing Data from Affymetrix MAS 5.0 Files
• Importing Data from CodeLink XML Files
• Importing Data from GenePix Files
• Importing Data from Genomic Solutions Files
• Importing Data from Quantarray Files
• Importing Data from ScanArray Files
• Importing Data from Affymetrix MAS 5.0 Files
• Merging Within-Chip Replicate Measurements
• Creating a Table View of Reliability Data
• Removing Values by Reliability Measure
• Importing Data from Tabular Files
• Importing Data from dChip xls Files
• Importing Multiple Files With One Sample Each
• Selecting the Gene Database Type
• Importing Multiple Files With One Sample Each
• Affymetrix Identifiers
• GenBank Identifiers
• UniGene Identifiers
• Performing Agglomerative Hierarchical Clustering
• Distance Metrics Overview
• Euclidean and Euclidean Squared Distance Metrics
• Manhattan Distance Metric
• Chebychev Distance Metric
• Spearman Rank Correlation Distance Metric
• Clustering Overview
• Agglomerative Hierarchical Clustering Overview
• Cancelling an Operation or Experiment
• Performing K-Means Clustering
• Distance Metrics Overview
• Euclidean and Euclidean Squared Distance Metrics
• Manhattan Distance Metric
• Chebychev Distance Metric
• Spearman Rank Correlation Distance Metric
• Glossary of Terms/Acronym List
• Disclaimer
• GeneLinker(TM) Product Suite
• GeneLinker(TM) Feature List
• Clustering Overview
• Cancelling an Operation or Experiment
• Export Partitional Cluster
• Tutorial 6: Introduction
• An Introduction to Classification: Feature Selection
• SLAM(TM)
• Changing Your User Preferences
• Cancelling an Operation or Experiment
• ANN Classification and Prediction Overview
• Classify New Data
• Creating an ANN Classifier
• Classification Plot Training Results
• MSE Plot
• MSE Plot
• SLAM(TM) Association Viewer
• Discretization
• Tutorial 6: Step 1 Import the Data
• Selecting a Template for Data Import
• Importing Multiple Files With One Sample Each
• Importing Data from Affymetrix MAS 4.0 Files
• Importing Data from Affymetrix MAS 5.0 Files
• Importing Data from CodeLink XML Files
• Importing Data from GenePix Files
• Importing Data from Genomic Solutions Files
• Importing Data from Quantarray Files
• Importing Data from ScanArray Files
• Importing Data from Affymetrix MAS 5.0 Files
• Tutorial 6: Step 2 Import Variable Data
• Importing Variables
• Tutorial 6: Step 3 Discretize the Data
• Tutorial 6: Step 4 Run SLAM
• System Specification
• Tutorial 6: Step 5 Display SLAM Association Viewer
• Tutorial 6: Step 6 Create a Gene List
• Tutorial 6: Step 7 Filter Datasets Using Gene List
• Tutorial 6: Step 8 Create an ANN Classifier
• Tutorial 6: Step 9 Classify Test Data
• Tutorial 6: Step 10 Display a Confusion Matrix
• Tutorial 6: Step 11 Display a Classification Plot
• Tutorial 6: Step 12 Set URL for Lookup Gene Operation
• Tutorial 6: Step 13 Lookup Genes
• Tutorial 6: Conclusion
• Tutorial 7: Introduction
• Tutorial 7: Step 1 Import the Data
• Tutorial 7: Step 2 Import Variable Data
• Tutorial 7: Step 3 Perform IBIS 1D LDA Search
• Tutorial 7: Step 4 View IBIS LDA Search Results
• Tutorial 7: Step 5 Display IBIS Gradient Plot
• Tutorial 7: Step 6 Perform IBIS 2D LDA Search
• Tutorial 8: Introduction
• Tutorial 8: Step 1 Import Affymetrix Data
• Tutorial 8: Step 2 Import Gene List
• Tutorial 8: Step 3 Set Gene Display Name
• Tutorial 8: Step 4 Import a Variable
• Tutorial 8: Step 5 Remove Genes With Poor Reliability
• Tutorial 8: Step 6 Estimate Missing Values
• Tutorial 8: Step 7 Perform F-Test and View Results
• Tutorial 8: Step 8 Gene List Filtering
• Tutorial 8: Step 9 Hierarchical Clustering
• Tutorial 8: Step 10 Display Matrix Tree Plot
• Tutorial 8: Step 11 Principal Component Analysis
• Tutorial 8: Step 12 Display 3D Score Plot
• Tutorial 8: Conclusion
• Tutorial 9: Introduction
• Tutorial 9: Step 1 Import the Data
• Selecting a Template for Data Import
• Importing Multiple Files With One Sample Each
• Importing Data from Affymetrix MAS 4.0 Files
• Importing Data from Affymetrix MAS 5.0 Files
• Importing Data from CodeLink XML Files
• Importing Data from GenePix Files
• Importing Data from Genomic Solutions Files
• Importing Data from Quantarray Files
• Importing Data from ScanArray Files
• Importing Data from Affymetrix MAS 5.0 Files
• Tutorial 9: Step 2 Import Variable Data
• Importing Variables
• Tutorial 9: Step 3 Create a SVM Classifier
• Classification Plot Training Results
• MSE Plot
• Tutorial 9: Step 4 Classify Test Data
• Tutorial 9: Step 5 Display a Confusion Matrix
• Tutorial 9: Step 6 Display a Classification Plot
• Tutorial 9: Conclusion
• Improved Outcomes: FAQ for GeneLinker and gene expression (microarray) and proteomics analysis.
• Improved Outcomes: Services for gene expression (microarray) and proteomics data analysis as well as software consulting for image guided surgery (IGS), bioinformatics and information technology (IT).
• Improved Outcomes, Software for Life, Kingston, Ontario
• Improved Outcomes: Image Guided Surgery (IGS) Consulting Services
• Improved Outcomes: Information Technology (IT) Consulting Services
• Improved Outcomes: Partners is microarray (gene expression) and proteomics analysis and image guided surgeryi (IGS).
• Improved Outcomes: Support page for GeneLinker software for gene expression and proteomics analysis.
• Improved Outcomes: Press on gene expression (microarray) and proteomics products as well as bioinformatics, image guided surgery (IGS) and informtaiton technlogoy (IT) consulting.
• Improved Outcomes: Press - Improved Outcomes Software Formed by Merger of Predictive Patterns Software and Visible Bytes Software
• Improved Outcomes: Press - Predictive Patterns Announces the Release of the Protein Biomarker Package for GeneLinker (TM) and GeneLinker (TM) Platinum 4.5
• Improved Outcomes: Press - Predictive Patterns Releases GeneLinker (TM) Gold and Platinum Version 4.5
• Improved Outcomes: Press - S2K's Team Chooses Predictive Patterns GeneLinker Products for Advanced Data Analysis
• Improved Outcomes, Software for Life, Kingston, Ontario
• Improved Outcomes: Press - Predictive Patterns Releases GeneLinker (TM) Gold and Platinum Version 4.0
• BioReprint062303_PROOF2.qxd
• Improved Outcomes: Press - Predictive Patterns Licenses GeneLinker Products and Technology
• Improved Outcomes: Press - Predictive Patterns Releases GeneLinker (TM) Gold Version 3.1 and GeneLinker (TM) Platinum Version 2.1
• Improved Outcomes: Sitemap