[Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control

[Chen-Yi Chen]

Hi all,
After going through all the ChIP-seq pipeline in ht-seq, I finally come down to normalization/peak calling. Interestingly, ht-seq seems to not have a standard normalization and peak calling algorithm between sample and control. I've read through the previous threads about "peaks calling," and people suggest all different things.
So I've tried the following packages:
chipseq -> using the cutoff as island/peaks calling, and there is nothing about normalization technique. From my understanding, I thought we need a normalized data from sample and control in order to do this, and I certainly don't know how to normalize them in ht-seq.
SPP -> didn't work, it returned a NaN out of range error when doing the enrichment (peak calling) calculation.
CSAR -> didn't seem to be available in installation through biocLite, but I downloaded and installed it manually. It didn't seem to work well with ShortRead. (at least I have no idea how to do it), and again, wig file output didn't visualize on UCSC genome browser.
ChIPseqR -> I didn't go in to it that much, but it seemed to be the "simulating package"
ChIPsim -> similar story as ChIPseqR
PICS -> I visited their website and they mentioned it should be available through bioconductor website, but I didn't see any PICS packages on bioconductor website.

Is there a standard (or simple) normalization technique/peak calling package in ht-seq that we can use?
I am not a statistician, so any suggestions on this normalization/peak calling would really help our analysis.

Thanks a bunch!

-Charlie-