Question: diffHiC with no biological replicates?
1
gravatar for hwick1
2.7 years ago by
hwick120
hwick120 wrote:

Is it possible, and is it statistically sound, to use diffHiC for differential HiC analysis when no biological replicates are available? I know edgeR lists a few options for calculating dispersion with biological replicates, but none of them seemed to good options. We can calculate dispersion for no bio reps with DESeq as well. But I'm less certain about whether it is possible (or statistically sound) to create the "fit" object from non-replicate data which diffHiC relies upon for the rest of the analysis (Ch. 6 onward). Has anyone tried this or know whether this is possible?

ADD COMMENTlink modified 2.7 years ago by Aaron Lun25k • written 2.7 years ago by hwick120
Answer: diffHiC with no biological replicates?
1
gravatar for Aaron Lun
2.7 years ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

It's as possible and as sound as RNA-seq data analysis without replicates - that is, not very. All of the comments in the edgeR user's guide pertaining to lack of replicates are similarly applicable to diffHic.

ADD COMMENTlink written 2.7 years ago by Aaron Lun25k
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