I used this workflow to analyze the Illumina microarray data, GSE35088. However, I did not obtain DE genes while GEO2R gave about 1000 DE genes. As I found that GEO2R does not perform the filtering step while when I filtered the probes (control probes, those with no symbol, and those that failed), only about 800 probes remained out of 22523 probes, is it usual or something is wrong?
Also, I guess the normalization step is different between the two workflows, yes?. so using GEO2R would not be safe for getting accurate results, is it right? kindly let me know if you have any suggestion/advice?