[BioC] Is it recommended to remove control probes for Agilent type data

[Ketaki]

I have Agilent 2 color data with 8635 probes, however both negative and positive
control probes comprise of 544 probes. If I remove control probes during
normalization I tend to get more differentially expressed probes as compared to
keeping the control probes suring normalization. Please advice me whether it is
recommended to remove control probes while normalization or not?

Summary of results
i)Using control probes while normalization
Upregulated probes 23
Downregulated probes 58

ii)Not using control probes while normalization
Upregulated probes 105
Downregualted probes 145

Regards 
Ketaki