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.
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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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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.
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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 default
Basic Expression Workflow
processes are given below.
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