Processes | Workflows | Expression QC Workflow

Expression QC Workflow
The Expression QC Workflow process runs a workflow to clean up and prepare raw expression data for further analysis. Options that enable you to specify methods for filtering, performing quality control, and normalization of your data are provided.
What do I need?
Two data sets are required for this process:
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.
The drosophilaaging.sas7bdat input data set and the drosophilaaging_exp.sas7bdat EDDS 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 Run, the Expression QC Workflow process begins by opening the Workflow Builder. The Workflow Builder builds settings files for each process, containing the information from the data sets and parameters specified in the Expression QC 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 QC and normalization processes are saved in the specified output folder, but are not displayed. Instead, a JMP journal is generated, providing links to the workflow dialog and the results of each process.
Click Open Workflow Builder Dialog.
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 Results 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 the default Expression QC Workflow processes are given below.