Hello everyone,

I am new in HTS data and there is a point that I don't really understand.

I want to analyse data from viability assays , for which I have positive and negative controls. So, I am interested in the quantity x_i / mean(x_controlPos) in order to select wells with less living cells than in control wells. I have tried all the normalisations provided by the package and it appears that the median normalisation with log-transformed data and a multiplicative model show the best performance. So finally I have negative and positive values.

When I am doing my ratio x_i / mean(x_controlPos), I have positive and negative ratio. I do not know how to interpret these negatives ratios !
So how to interpret these "negatives ratios" or am I doing wrong my analysis ?

Thanks a lot for your help !

Hi, you are right to be untrusting of these ratios. As your data is now on a log-scale, you should now be looking at differences from your controls i.e. x_i - mean(x_controlPos). This is because of the mathematical properties of logarithms, since log(x/y)=log(x)-log(y).