Hi all,

I am using the Nimblegen expression microarray. Each array has 4 different
bacteria genome, and the position of probes are randomly assigned. I have
two groups: control and treatment, and I used the mixed RNA from 4 bacteria
under each condition to apply to array. However, the quantity of RNA from 4
bacteria may be different, and the difference is not consistent between
control group and treatment group. Should I normalize separately for each
bacteria? And if yes, what's the proper way to do that? Can I take the raw
calls file provided by Nimblegen for each bacteria and then apply quantile
normalization?

Thanks for help.
Xiao

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