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Dear there,
Is it expected to get negative tag count by using DESeq2?
I am using HOMER (getDifferentialPeaksReplicates.pl http://homer.ucsd.edu/homer/ngs/peaksReplicates.html) for my analysis, which uses R/Bioconductor and DESeq2 (by default) to perform the differential enrichment calculations. Why did I get 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 |
Does it attribute to "normalization factor"? If using this, is it expected to get negative tag counts (I am running without it now)?
Thanks a lot!
I did send an email and cross my fingers to get response from them.
Here is the command that I used for HOMER, it is very easy and just one-line command.
getDifferentialPeaksReplicates.pl -t IP1_tagDir IP2_tagDir IP3_tagDir -i Inp1_tagDir/ Inp2_tagDir/ bInp3_tagDir/ -genome AGPv3 -gsize 2.2e9 > ../getDiffPeaksRep/Ip_Inp_peaks.txt
We can't get the DESeq2 code from the one-line command. I tried to look the Perl code and tried to print out the deseq2 command, but not successful so far.
I feel so frustrated to get negative tag counts :-(
Thanks a lot!