geWorkbench

Design and outline of tutorials for geWorkbench

Tutorial Design considerations - 1. Probably best not to use detailed section numbers, since we cannot autoupdate them in this wiki. Instead, rely on links? 2. Each section should list example data files needed, and these should be part of distribution.

Outline for tutorials

        2.1 Before You Begin
        2.2 Getting Started
             Is caWorkbench downloaded and installed?  Link to download and installation
             Important concepts:
                 Use of activated phenotype and marker panels throughout application.
                      What is default active set if no panels are active?
                      Note that there is a new "plot" button that is available only when a gene panel is active.
             The  menu bar - point out that some commands are available both from the menu bar and by right-clicking on a dataset....
        

        2.3 Loading Data
             2.3.1 File types supported
                    Expression
                       Affymetrix MAS5/GCOS (text files output by Affymetrix software)
                       Affymetrix File Matrix (.exp)(a geWorkbench defined format)
                       RMAExpress Processed File
                       GenePix
                       Note - the type "Normalized no-confidence expression matix" has switched the phenotype and gene labels -don't use until fixed.
                    Genotypic
                       Genotypic data files - is this working?
                    Sequence
                       Fasta
                    Pattern Detection
                       Pattern Files

             2.3.2 Loading MAS5/GCOS type files
                        Use the 10 cardiomyopathy files from Harvard.
                        What happens the first time a new chip-type is loaded - how long does it take, what is happening, what internal files are being built?
             2.3.3 Merging loaded data
             2.3.4 Loading matrix format files
                        Include webmatrix2000G?, webmatrix4000G? and webmatrix.exp?
                    Note - explain matrix format in an appendix
             2.3.5 Other file types supportedLoading RMAExpress files
                    Must generate an example RMAExpress file, start with harvard cardio files?
        2.4 Working with Marker and Phenotype Panels
                    Use the cardiomyopathy dataset created in 2.3
               2.4.1 Creating Phenotype Panels
               2.4.2 Assigning Case/Control status
               2.4.3 Activating a phenotype panel
               2.4.4 Creating Gene/Marker Panels
               2.4.5 Activating a phenotype panel
        2.5 Saving data files
               Use the cardiomyopathy dataset annotated in 2.4
               2.5.1 Save to matrix file
               
                 

         2.5 Visualize Gene Expression
         2.6 Filter and Normalize Data
               2.6.1 Normalize
               2.6.2 Filter
         2.7 Clustering Gene Expression Data
         2.8 Differential Expression
               2.8.1 T Test
         2.9 Regulatory Network
         2.10 Integrated Annotation Information
         2.11 Enrichment Analysis
         2.12 Sequence Analysis
         2.13 Pattern Discovery
         2.14 Promoter Analysis