Hi everyone,

Although this question is more related to ChIP and ChIP-seq, it could be
probably anchored in a more general statistical context.

The question is : what method is better  to assess the significance of the
change  in a signal (the signal can be DNA binding, for instance) given the
background and 2 conditions.

<. condition1 (eg no treatment) :  background = 1;
                                                signal = 5;

<. condition2 (eg hormonal treatment) : background = 3;
                                           signal = 6.

The methods can be :

a. substract the background : i.e. (signal_treatment - background_treatment)
/ (signal_no_treatment - background_no_treatment)

b. calculate the fold change: i.e. (signal_treatment / background_treatment)
/ (signal_no_treatment / background_no_treatment)

c. any other method ? i.e. (signal_treatment - signal_no_treatment)  / (
background_treatment - background_no_treatment)

Thank you very much.

Bogdan

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