Genomic data sets often contain values or
observations
that deviate substantially from expected values. These deviations can often be ascribed to a variety of technical or other
factors
, that have little to do with biological cause and effects. In these situations, it is often better to identify and exclude outliers from an analysis than it is to include them, particularly where the cause of the anomalies can be explained by technical problems.
Often, valuable information about the quality of an array can be obtained from a visual examination of an image of the hybridization pattern. The
Surface Summary
process works with three dimensional data, with
variables
denoted
X
,
Y
, and
Z
. You can specify any number of
Z
variables to be plotted over common
X
and
Y
variables. The process summarizes the
Z
variables over gridded blocks of the
X
and
Y
variables and then creates a surface plot over the grid. You can optionally smooth the surface or subtract it from the original
Z
data. For example, you can use this process to perform spatial background correction for
microarray
data.
The first required data set, the
coordinate data set
, lists the
x-
and
y-
coordinates for each spot on the arrays. The
probemap_u95a.sas7bdat
data set, used in the following example, is shown below.
The second required data set,
the
input Z data set
, contains all of the numeric
Z
value data (intensities) to be analyzed. The sample data set used in the following example, the
chips45and55.sas7bdat
data set, shown below, is from the Affymetrix Latin Square experiment that is described in
Sample Case Studies
. This data was
originally generated by Affymetrix Corporation to develop and validate their U95A GeneChip and Microarray Suite (MAS) 5.0 algorithm over a range of known concentrations. Each group in the experiment contains a pool of non-specific
RNA
as well as a set of 14 distinct human
transcripts
spiked in at known concentrations. Intensity data are listed in the last two columns of the data set.
The
probemap_u95a.sas7bdat
coordinate data set and the
chips45and55.sas7bdat
input Z data set, 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
.
The output generated by this process is summarized in a Tabbed report. Refer to the
Surface Summary
output documentation for detailed descriptions and guides to interpreting your results.