[Bioc-sig-seq] a general question

[Martin Morgan]

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
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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