I have two tricky questions and I appreciate any useful comment
1- I have 6 samples , 3 control (two of them are biological replicate) and 3 treated (two of them are biological replicate). How should I use them for pathway analysis ? for example does it make sense to do like this ?
Average the three control (A) , average the three treated replicate (B), then B/A ==> fold change is this right?
1- which pathway analysis is giving the statistical differences for a pathway, for example with IPA , you can say is a pathway significantly expressed by a set of genes or not based on p-value and z but is there any other pathway analazor which gives such results ?