Variance Filter
Parameter Information
The variance filter allows the removal of genes with low variation of expression over the
loaded samples. This filter is basically used to remove ‘flat genes’ that don’t vary much
in expression over the conditions of the experiment. The variance filter has three possible
criteria for specifying which genes to keep. The Enable Variance Filter check box turns the
filter on and off. Be sure to observe the History Node log to see the number of genes
retained after using the filter. Note that the variance filter is performed after other
filters such as Percent Cutoff Filter is imposed. This convention insures that the genes
that are tested for variance also contain some minimum level of ‘good’ (not missing) data.
Percentage of Highest SD Genes
The Percentage of Highest SD Genes option ranks the genes based on standard deviation and
then the genes that are kept are some percentage of this ranked list. For and example,
if we have 1000 genes and the percentage was set to 20%, then the result would be a
final list of the 200 most variable genes.
Number of Desired High SD Genes
The Number of Desired High SD Genes option also ranks the genes based on SD and
then the number of genes specified are selected from this SD ordered list such that
the highest SD genes are selected.
SD Cutoff Value
The SD Cutoff Value option uses an actual SD value such that all genes having
an SD greater than this value are selected.