Number of peaks with Zinba

[spacup]

Hi everybody,

I ran a ZINBA analysis for FAIRE-seq study and found around 4,000 peaks... which seems to be very few as we should find around 100,000 according to this paper : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202292/

So I was wondering if somebody could has an idea why I found so few peaks?
(See below the options)
Thanks for your help!

run.zinba(
align='.../athresh1_ext134',
numProc=8,
seq=.../file.bed',
basecountfile='.../file.basecount',
filetype='bed',
outfile='.../output',
twoBit='.../GRCh37.2bit',
extension=134,
printFullOut=1,
refinepeaks=1,
input='none',
threshold=0.05,
FDR=T,
interaction=T,
selectchr='22',
selectcovs=c("gcPerc", "align_perc", "exp_cnvwin_log"),
selectmodel=T
)

[aaronh]

it look like you only ran it on chr22

[spacup]

No, I checked the peaks in IGV and there are in all chromosomes...

The option selectchr='22' is just use for model selection

[spacup]

Nobody has an idea?
Because I downloaded ENCODE FAIRE-seq data and I used ZINBA for peak calling and althought ENCODE find around 200,000 peaks (with Fseq) I only found around 60,000...
I know they used p-value whereas I used FDR in ZINBA which is more stringent and that could be an explanation, but they fit their data to gamma distribution and I don't really understand the meaning of this...

Can anyone enlighten me?
Has anyone tried ZINBA on ENCODE data?
thanks