Process Description

Filter Intensities

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 exclude outliers from an analysis, particularly where the cause of the anomalies can be explained by technical problems, than it is to include them.

The Filter Intensities process can be used to replace measurements that lie outside of a typical range of values from a data set, as determined by comparisons using within-condition intensity percentile or values. It can also be used to filter out rows that have consistent poor performance across many conditions in an experiment, as judged by statistical measures of intensities, including mean, median, interquartile range, and percentile.

What do I need?

Any SAS data set containing numerical intensity variables.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output generated by this process is summarized in a Results window. Refer to the Filter Intensities output documentation for detailed descriptions and guides to interpreting your results.