SAS data sets are typically formatted in one of two ways:
wide or tall
. In wide data sets
, samples are listed in columns, and molecular entities, such as genes or proteins, are listed in rows.
Tall
data sets are the transpose of
wide
data sets, with molecular entities listed in columns and samples listed in rows. A
tall
data set has one or more common feature identifiers (ID column(s)) across columns of interested measurements. Typically, the number of rows is greater than the number of columns in this format of data sets. Analyses of
tall
data sets typically also require an additional
Experimental Design Data Set (EDDS)
. Different procedures in JMP Genomics have different requirements for data set format. Please refer to
Data Sets Used in JMP Genomics Processes
for a more detailed description of these data set formats.
Many SAS procedures (
PROCs
), however, require that input data sets be formatted in a
stacked
format. A
stacked data set
has all of the
observations
of interest stacked into a single
variable
, or column. Rows are organized into groups of similar observations in which each row in the group differs in only one experimental parameter. Each group differs from other groups in additional parameters. A stacked data set typically has many, many more rows than columns.
The
Stack
process combines and restructures a
tall
formatted SAS data set with an accompanying EDDS into a
stacked
format. This process enables you to quickly get your data into a stacked format for directly running (or testing) SAS processes.
Two data sets are
required
for this process:
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An
Experimental Design SAS Data Set
. This data set tells how the experiment was performed, providing information about the columns of the primary experimental data. See
Experimental Design Data Set (EDDS)
for more information.
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The
affylatin_norm.sas7bdat
data set (found in the \
LifeSciences\Sample Data\Microarray\Affymetrix Latin Square
directory included with JMP Genomics and JMP Clinical, and described in
Affymetrix Latin Square Data
) serves as an example
Input SAS Data Set
.
The
affylatin_exp.sas7bdat
data set (found in the \
LifeSciences\Sample Data\Microarray\Affymetrix Latin Square
directory included with JMP Genomics and JMP Clinical, and described in
Affymetrix Latin Square Data
) serves as an example
Experimental Design SAS Data Set
.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The output of the
Data Stack
process includes a
Results
window, which lists the name of and path to the
Output Stack Data Set
. To best visualize this data set, think of the
Experimental Design SAS Data Set
as a scale diagram used to guide the unpacking of the “boxy” 1604x59-data cell structure (the intensity data in the
Input SAS Data Set
) into a 94636x1 tower.
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