The Basic Expression Workflow process builds and runs a workflow using an expression data set. This automated process uses one or more quality control processes and normalization methods, followed by ANOVA, to perform a basic expression analysis.
|
•
|
An Input Data Set that contains all of the numeric data to be analyzed. The drosophilaaging.sas7bdat data set, from the Drosophila Aging experiment described in Drosophila Aging Experimental Data, serves as an example, and is partially shown below. It has 49 columns and 100 rows. Note that this is a tall data set; each probe corresponds to one row whereas each column corresponds to a separate experimental condition.
|
|
•
|
An Experimental Design Data Set (EDDS). This data set tells how the experiment was performed, providing information about the columns in the input data set. The drosophilaaging_exp.sas7bdat EDDS serves as an example, and is shown below. Note that one column in the EDDS must be named ColumnName and the values contained in this column must exactly match the column names in the input data set.
|
A third data set, the Annotation Data Set, is optional. This data set contains information such as gene identity or chromosomal location, for each of the markers. The drosophila_annotation.sas7bdat data set serves as an example, and is shown below.
The drosophilaaging.sas7bdat input data set, the drosophilaaging_exp.sas7bdat EDDS, and the drosophila_annotation.sas7bdat annotation data set are located in the Sample Data\Microarray\Scanalyze Drosophila directory included with JMP Genomics.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
When you click , the Basic Expression Workflow process begins by opening the Workflow Builder. The Workflow Builder builds settings file for each process containing the information from the data sets and parameters specified in the Basic Expression Workflow dialog. Once the setting files are generated and saved, the individual processes in the workflow are sequentially opened, populated, and run. The results of the processes are saved in the specified output folder. Finally, a JMP journal is generated, providing links to the workflow dialog and the results of each process.
|
Click .
|
The Workflow Builder dialog shows the settings for each of the processes in the workflow. You can select and edit individual settings to adjust your analysis.
|
|
Clicking each of the buttons on the journal brings up the output of each of the processes. This enables you to examine each set of output so that adjustments can be made to the individual settings, as needed. For your convenience, links to default Basic Expression Workflow processes are given below.
|
|
•
|