The
Loess Normalization
process normalizes data across arrays using a loess smoothing
model
. You can use the average across arrays and channels as the baseline for
normalization
or you can specify one array and channel to be used as the baseline.
Note
: If you want to perform within-array
loess normalization
for two-channel arrays, run the
Ratio Analysis
process, instead.
The first data set, the
Input Data Set
, contains all of the numeric data to be analyzed. This data set must be in the
tall
format where each sample corresponds to one row and each column corresponds to a separate experimental condition or array.
The
drosophilaaging.sas7bdat
data set, shown below, is a normalized data set derived from the
Drosophila
Aging experiment described in
Sample Case Studies
. It has 49 columns and 100 rows corresponding to 49 arrays and 100 individual
probes
, respectively.
The second data set is the
Experimental Design Data Set (EDDS)
. This required 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
drosophilaaging_exp.sas7bdat
EDDS, is shown below. Note that the
ColumnName
column lists the column names in the input data set. The
Array
column corresponds to an
index variable
. Note the
variables
describing experimental conditions.
A third, optional data set is the
Baseline Reference Data Set
. A baseline reference data set is generally used when you have a large set of reference arrays and you would like to add a few new arrays to an existing
distribution
. This data set should be in the
tall
format and contain both a baseline reference column and columns to merge with the input data set.
The
drosophilaaging.sas7bdat
and
drosophilaaging_exp.sas7bdat
data sets are included in the
Sample Data
folder.
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
Loess Normalization
output documentation for detailed descriptions of the output of this process.