I am currently working with gene expression data where I have a number of genes (variables) measured over a number of samples. I could not make sense of the statistics and visualization suite we have, so I started checking out the tutorial and came up with the following bit:
You specify a lower cutoff for the variance. You can either enter a value, or use the slider. The value is relative to the variance of the variable with the largest variance. The variance is calculated over the active samples.
Example: If you select the value 0.1, then all variables that have a variance σ greater than or equal to 0.1 ·σ_max are kept, where σ_max is the variance of the variable with the largest variance.
I realize that it might be very fundamental question, but why would I want to filter my variables based on the variation alone? What I would want to know is which variables "explain" the difference between the samples (which are hypothesized to belong to a couple of different biological conditions)