Dear all,

I make a differential expression analysis using t test by multtest package in R under conditions of p-value < 0.05. So the output of this step is group of genes with significant p values and partially significant p adjusted values as shown in this link:

I used this output as an input for the pathfindR and there is p_threshold parameter whose default value is 0.05. So, the best way to get the pathways of all differential expression genes to increase this threshold or keep it as 0.05 and neglect the genes whose p adjusted is greater than 0.05 ?

Thanks in advance