Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?
Answer from @llrs, converted from comment:
Probably is a question for the maintainer but I would guess that is a variance of the gene in the control dataset. So, if in normal samples the gene has a standard deviation of 0.5 this is the expected too in the tumoral cells. calculate the sd only on the control samples. So if the healthy/control samples have such variation the altered ones should have these or more according to the article (if I understand it correctly).
std &lt;- apply(data[, controls], 1, sd, na.rm = TRUE); quantile(std, 0.25) should be much faster and efficient
But  I would check it in support.bioconductor with the authors/maintainers.