Hello, I am quite comfused about the mechanism and detailed process of background normalization in diffbind normalization. As the manual depicted,
"The core background normalization technique is to divide the genome into large bins and count overlapping reads. As the enrichment expected in ChIP-seq (and ATAC-seq) is expected to occur over relatively narrow intervals (roughly between 100bp and 600bp), it is expected that there should not be systematic differences in signals over much larger intervals (on the order of 10,000bp and greater). Any differences seen should be technical rather than biological, so it is safer to normalize based these differences."
But by which value can we do the normalization ?
Thanks a lot!
data(tamoxifen_analysis)
> tamoxifen <- dba.normalize(tamoxifen, method=DBA_ALL_METHODS,
+ normalize=DBA_NORM_NATIVE,
+ background=TRUE)
> tamoxifen <- dba.analyze(tamoxifen, method=DBA_ALL_METHODS)