Most of the processes in JMP Genomics assume that the input SAS data set has a particular data structure. JMP Genomics distinguishes between
tall
and
wide
SAS data sets. A
tall
SAS data set has samples as columns, and molecular entity (such as marker, gene, clone, protein, or metabolite) as rows. A
wide
SAS data set is the transpose of a
tall
data set, having the samples as rows and molecular entity as columns. When specifying the input SAS data set for a process, it is important to know the required form. Most of the processes associated with genetic analyses require a
wide
structure, whereas most of those for
microarray
and proteomics analyses use a
tall
structure.
The
Transpose Tall to Wide
process transposes a SAS data set in
tall
format, along with an accompanying experimental design table, into a data set in
wide
format in which the rows and columns are transposed.
Caution and Tip
:
Wide
data sets can become unwieldy when there are thousands of columns. In this case, it can be more efficient to first use other analytical processes to reduce the number of rows in a
tall
input data set. For example, use
Statistics for Columns
to reduce the number of rows in the original data set by computing a summary statistic,
K-Means Clustering
to cluster the rows into similar groups, or
Merge
/
DATA Step
to extract a subset of the rows.
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•
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The
tall
Input Data Set
to be transposed, such as the
affylatin_norm.sas7bdat
data set (found in the
LifeSciences\Sample Data\Microarray\Affymetrix Latin Square
directory included with JMP Genomics, and described in
Affymetrix Latin Square Data
) shown
below
. This is a
tall
data set with individual arrays listed in 59 data columns and
probesets
listed in the 1604 data rows.
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T
he
Experimental Design Data Set (EDDS)
. This required data set tells how the experiment was performed, providing information about the columns of the primary experimental data.
The
affylatin_exp.sas7bdat
EDDS
(found in the
LifeSciences\Sample Data\Microarray\Affymetrix Latin Square
directory included with JMP Genomics, and described in
Affymetrix Latin Square Data
)
is shown
below
.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The wide SAS data set generated by this process is listed in a
Results
dialog
that is displayed in a new window.
|
Click
to view the output wide data set.
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The data has been transposed; there are now 1604 data columns and 59 data rows. In addition, the
_wid
suffix has been appended to the transposed filename.