Dear all, I want to find differential expressed genes between cancer and adjacent normal tissues from large number of microarray data sets (52).
Each data set consists of large number of samples of affymetrix or agilent platforms.
I don't have access to server at the moment and I want to know if I can get the list of DEGs for each sample separately and then obtain the overlap between these 52 data sets.
I know removing batch effects is of great significance before integrating the results of these studies, but I want to know how much not performing it affect the results.
I will appreciate any comments