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

Question

[The]

Hello All,

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

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

Answer 1

[Carlo Yague]

In this case, the best is to use spike-in to normalize between your conditions. If this is not possible, an alternative could be to select a class of genes (ex: snoRNAs) or a few housekeeping genes as normalizers.