Scaling before anova?

I want to perform an anova analysis for identifying differentially expressed genes. 开发者_如何学CShould I scale the data using quantile normalization or median absolute deviation before looking for differentially expressed genes or should I apply anova directly on data obtained through RMA?

Thanks a lot in advance

You can apply ANOVA after RMA, since it includes background adjustment, summarisation and quantile normalisation steps (see here). For non-Affy data, something along the lines of log transformation/quantile normalisation or VST (variance stablilising transformation)/RSN (robust spline normalisation) for Illumina data could be used prior to ANOVA.

Best place for this question, as already pointed out is BioStar.

By the way you will also want to do some filtering on the data after RMA and prior to ANOVA to remove probesets of low variance. If you're working in R you will want to look at genefilter.

Always, always normalise, your results are simply not comparable otherwise. The normaisation technique to use depends largely on the microarray technology you are using.

For a more in-depth answer, you should try the Biostar Stack Exchange site.