I'm currently mining 21 microarrays of tumor samples after chemotherapy. The response of the tumor from the chemotherapy is graded by Good or Poor depending on the percentage of necrosis of the tumor. There are 10 "Good" and 11 "Poor" ranked samples. I want to find out the differentially expressed genes(DEGs) behind the "good" or "poor" response.
However, after processing the data using the rma function of affy package in R and determining the DEGs by using SAM. No positive gene showed up. The SAM plot is like that (please see fig.) ![SAM plot] : https://ibb.co/nsyV35 There are actually over 600 DEGs lFClog1.5l>1 when ignore the FDR.But when concerning FDR, none of then are less the 0.05. T_T
I would really appreciate it if some could answer me that what makes a SAM plot like that happen? Biological replication?individual bias? Is there any step-back I can make on it?