Dear folks,
Does anyone have experience using getDifferentialPeaksReplicates.pl in HOMER, which is new added to HOMER in this Feb. It uses R/Bioconductor and DESeq2 (by default) to perform the differential enrichment calculations. But, I don't know why I got negative tag count for my results? I pasted some of lines from the results:
Inp1_tagDir Tag Count in given bp (14503111.0 Total, normalization factor = 1, effective total = 10000000) Inp2_tagDir Tag Count in given bp (15163786.5 Total, normalization factor = 1, effective total = 10000000) Inp3_tagDir Tag Count in given bp (14010122.5 Total, normalization factor = 1, effective total = 10000000) IP1_tagDir Tag Count in given bp (13945492.5 Total, normalization factor = 1, effective total = 10000000) IP2_tagDir Tag Count in given bp (11841367.0 Total, normalization factor = 1, effective total = 10000000) IP3_tagDir Tag Count in given bp (15415780.0 Total, normalization factor = 1, effective total = 10000000) -0.288246836848404 0.433387837255659 -0.268014291397154 1.7191399108166 2.70673888043271 1.86558388806041 0.446205758005484 -0.342275173587881 -0.296143075827782 1.39627776477782 2.12637915698719 2.54507683196772 0.695292076927187 -0.0274159575070236 0.72292223174561 2.79295984906655 2.83354767081108 2.21324718854021
I believe it's not possible to obtain normalized counts from DESeq2 that are negative.
https://support.bioconductor.org/p/98855/
HOMER is of much power for NGS data analysis but I don't see there is a group that the community can discuss questions. Any one have an idea will be really appreciate, thank you so much!
