I am analyzing a GEO dataset of platform (GPL17077) Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray. I followed the steps given in LIMMA user guide 2016 (page number 110-112). The protocol given there is for Agilent 4x44K Arrays. So my question is whether i have to filter out control probes and low expressed probes for the "platform SurePrint G3 Human GE v2 8x60K Microarray" ?
I opened the GPL file GPL17077 and found that there are only 1 negative control and more number of postive controls (more than 50 approx).
I performed the DEG analysis in both the ways by filtering out the low expressed probes and without filtering out the low expressed probes. And I found that more DEGs are obatined when i filtered the low expressed probes.
Also, I have 10 control array and 9 test arrays. So can i keep probes at atleast 10% brighter than negative controls on 9 arrays only ?