Normalization of log-fold-change ratios when there is a global shift in expression

[august]

Usually, for test vs control studies of comparative gene or protein expression , we assume that the there is NO major difference in global gene expression between the control and the case. Accordingly,as a data normalization procedure, log expression ratios of case/control is often median or mean shifted so as to bring the average log-ratio to zero .

However there can be some cases where there is indeed a shift in global gene /protein expression and such meadin/mean centering doesn't hold good.

I wish to know if there are any centering and/or other normalization techniques available for such kind of globally shifted data.

Thanks