Hi, Using DESEQ2 and EDGER in diffBind gives huge difference in total number of differentially bound sites around 8000 for DESEQ2 and around 700 for EDGER, reading the vignette, the number should be fairly similar. And also do we need to use "DBASCORETMMREADSFULL" in dba.count if I am setting "bFullLibrarySize=TRUE" in dba.analyze? Currenlty I am using "DBASCOREREADS" in dba.count with "bFullLibrarySize=TRUE" in dba.analyze.
When there is a big difference like that, it is usually down to the different normalization methods.
bFullLibrarySize=TRUE, the DESeq2 analysis will perform only a basic normalization to library size, while the edgeR analysis will perform a more substantive adjustment. If there is a large change in one direction, the simple normalization is usually better.
You can look at what is going on using
dba.plotMA(). Compare the plots with
bNormalized=FALSE to one with
bNormalized=TRUE for both
Regarding the score to use in dba.count(), it doesn't matter for the analysis. The score is only used for global plots; when you run
dba.analyze(), it re-does whatever normalization you've specified in the