A note on thresholding
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Davide Cittaro
Apr 29, 2011, 3:05:48 PM4/29/11
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Hi all,
just a chime on thresholding step. dspchip can perform thresholding of your data at profile or peak level. What does it mean? If you specify letter 'T' in analysis pipeline, profile data (i.e. the wiggle) will be thresholded and the same information will be used to find peaks and to score them. You may also not specify 'T' in the pipeline and apply thresholding only at peak detection time. The difference is that the profile (that you'll display in any browser) will contain some "background" that will be used to correctly score peaks. To sum things up: if you need to find enriched regions, it may be better to avoid thresholding in the pipeline and enabling later (with the "--threshold" option). I'm going to somehow unify/fix this odd behavior soon.
just a chime on thresholding step. dspchip can perform thresholding of your data at profile or peak level. What does it mean? If you specify letter 'T' in analysis pipeline, profile data (i.e. the wiggle) will be thresholded and the same information will be used to find peaks and to score them. You may also not specify 'T' in the pipeline and apply thresholding only at peak detection time. The difference is that the profile (that you'll display in any browser) will contain some "background" that will be used to correctly score peaks. To sum things up: if you need to find enriched regions, it may be better to avoid thresholding in the pipeline and enabling later (with the "--threshold" option). I'm going to somehow unify/fix this odd behavior soon.
d
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Davide Cittaro, PhD
Davide....@iit.it
Center for Genomic Science of IIT@SEMM
Via Adamello 16, 20139 Milan
t: +39 02 574303007
f: +39 02 57489937
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