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.