Hi Bogdan -- Bogdan Tanasa <[email protected]> writes:
> 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) Ratios, especially with background in the denominator, can be very bad, as the denominator is close to zero and estimated poorly -- the resulting ratio varies greatly but for the 'wrong' reason (sampling variation in background, rather than systematic variation in foreground). Here's a recent discussion of additional ChIP-seq specific approaches http://www.nature.com/nbt/journal/v26/n12/abs/nbt.1508.html Martin > c. any other method ? i.e. (signal_treatment - signal_no_treatment) / ( > background_treatment - background_no_treatment) > > Thank you very much. > > Bogdan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
