run_spp or run_spp_nodups

[Mattia Forcato]

Dear Anshul,
I am trying to use IDR pipeline, in particular I want to call peaks with run_spp.r. I am using R-2.15.1 and the version of spp contained in ccQualityControl.v.1.1.tar.gz. I get the following error soon after the reading of the input files:

Error in names(cc) <- names(otl) : attempt to set an attribute on NULL
Calls: get.binding.characteristics
Execution halted

I noticed that if I use run_spp_nodups.r from http://code.google.com/p/phantompeakqualtools/  I don't get this error. My ChIP .bed files are in fact without duplicates although this is not the case for the control which is the concatenation of 2 replicates. By inspecting the 2 scripts I saw that they differ just by the value of the remove.tag.anomalies parameter in get.binding.characteristics function and by a different number in the calculation of ph.peakidx (1.5 instead of 2) in line 763.
I would like to know if it is correct to use the run_spp_nodups.r script for my files and to use files where the replicates have been removed or it is another kind of problem.
Sorry if this topic has already been discussed.
Best regards,

Mattia Forcato
--
Mattia Forcato, PhD
Center for Genome Research
Dept. of Life Sciences
University of Modena and Reggio Emilia
Via G. Campi, 287
41125 - Modena - Italy
lab: +39-059-205-5454