I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset.
As I was reading the documentation of the pathifier, in order to configure it properly for my dataset, I saw that for the
min_std argument they suggest to use the technical noise.
min_std: The minimal allowed standard deviation of each gene. Genes with lower standard deviation are divided by min_std instead of their actual standard deviation. (Recommended: set min_std to be the technical noise).
But how am I going to calculate it ? At first run I just used the value
0.2254005 from the example they provide with that package, but this might not be the right for my dataset.
So from here it says:
The minimal standard error (min_std) was set as the first quartile of the standard deviation in the data. How am I supposed to calculate this first quartile of the std? Any idea? Should I calculate the sd() for each gene and then find the first quartile?
What do you think about this function?