Hello, I created normalized affymetrix data from raw .cel files available at gene expression omnibus by following steps mentioned here: http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html.
I can see that the groups do not differ much (which is very surprsing as there are controls and disease samples). More worriesome part is that there are many multiple entries for some genes. What might have gone wrong? How to handle these multiple entries?
Gene annotation for affymetrix entries was obtained using the last steps mentioned in the tutorial above.