I am using microarray (GSE38642) database,that includes 54 non-diabetic and 9 diabetic islets samples, platform ( Affymetrix Human Gene 1.0 ST Array).
I used Bioconductor to mining the data and I got 8500 DEGs. Now I want to select the top up- and down-regulated genes.
I am not sure what I have to do for example I used:
FC_thresh = 10 and pvalue_thresh= 1.2e-8 to selcet the top up-regulated genes according to the formula:
(DES>=FC_thresh && DES<pvalue_thresh).
what have I done with down-regulated?
I am new in this field. any help will be highly appreciated