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.
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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.
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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.
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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
, 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.
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Click
.
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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.
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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 the default
Expression QC Workflow
processes are given below.
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