[Bioc-sig-seq] a general question
Martin Morgan
mtmorgan at fhcrc.org
Sun Mar 8 16:47:02 CET 2009
Hi Bogdan --
Bogdan Tanasa <tanasa at gmail.com> 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]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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Phone: (206) 667-2793
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