The
Data Standardize
normalization
process standardizes values of
numeric variables
in a SAS data set. A large number of potential methods are available for performing the
standardization
.
One data set is
required
for this process: the
Input Data Set
that
contains all of the numeric data to be analyzed.
The
drosophilaaging.sas7bdat
data set from the
Drosophila
aging experiment of Jin, et al. (2001) that is described in
Drosophila Aging Experimental Data
and used in the example that follows,
is shown below (and included in the
Sample Data
folder that comes with JMP Genomics). It has 48 data 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.
|
•
|
The
Experimental Design Data Set (EDDS)
. The
drosophilaaging_exp.sas7bdat
EDDS is shown below. This data set tells how the experiment was performed, providing information about the columns in the input data set. 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
Standardization Statistics Input SAS Data Set
(not shown). This data set is used when selecting
DATASET
as the
Standardization Method
. It contains location and scale estimates by which to standardize the input data set.
|
|
•
|
The
Drosophila
aging experiment of Jin, et al. (2001) consists of 24 two-color cDNA
microarrays
, six for each experimental combination of two lines (Oregon and Samarkand), two sexes (Female and Male), and two ages (1 week and 6 weeks). The
Cy3
and
Cy5
dyes were flipped for two of the six replicates for each
genotype
and sex combination. The design is a split-plot design, with
Age
and
Dye
as subplot
factors
, and
Line
and
Sex
as whole-plot factors. A total of 4256 clones were spotted on the arrays, but for this example, we use a subset containing 100 randomly selected genes.
The raw data from this experiment were evaluated using
distribution
analysis. The
Parallel Plot
(shown below) provides the raw univariate distributions of all 48 channels from the 24 arrays.
|
Select
MEDIAN
as the standardization method to follow this example.
|
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
Refer to the
Data Standardize
output documentation for detailed descriptions of the output of this process.