[BioC] loged data or not loged previous to use normalize.quantile

[Marcelo Luiz de Laia]

Dear Bioconductors Friends,

I have a question that I dont found answer for it. Please, if you have a 
paper/article that explain it, please, tell me.

I normalize our data using normalize.quantile function.

If I previous transform our intensities (single channel) in log2, I dont 
get differentially genes in limma.

But, if I dont transform our data, I get some genes with p.value around 
0.0001, thats is great!

Of course, when I transform the intensities data to log2, I get some NA.

Why are there this difference? Am I wrong in does an analysis with not 
loged data?

Thanks a lot

Marcelo