Normalisation issue?
 

Hi,

I'm quite new to microarray analysis and was hoping to get some thoughts on an issue I'm having.

I have results from Mouse Gene ST 1.0 chips, essentially grouped into tumour and non-tumour samples. I get a weird result when looking at my differentially expressed probes, I have 5 upregulated out of the first 500 listed.

I was wondering if this could be a normalisation issue.

When I look at the signal histogram from the chips after normalisation (attached) with affymetrix expression console I can see that the histograms don't overlap. My interpretation of this is that the samples aren't normalising. Is this correct? Is this why I'm getting my strange result? What can I do to overcome this issue?