Any way to quantify the variation of genes that expressed in Affymetrix expression data?
You can use the following code to calculate the coefficient of variation:

# expr is your expression matrix.
SD &lt;- apply(expr, 1, sd)
CV &lt;- sqrt(exp(SD^2) - 1)


It might be implemented in some package but it is so brief that you can write it again yourself. Then you can filter out those that are below certain percentage of the distribution of CV (like 0.1)

expr[CV &gt; quantile(CV, probs = 0.1), ]