Question: diffBind analysis: only one replicate
0
gravatar for danielaperry2015
10 weeks ago by
danielaperry20150 wrote:

Hi there,

I am trying to use diffBind to obtain a set of consensus peaks and fold changes for three different transcription factors chipped. I am comparing WT vs. mut, with one gene knocked out in mutant. For one of the transcription factors, I only have one replicate as the second replicate has failed. As a result, I am getting errors from diffBind. Any advice on how to proceed? Thank you.

chipseq diffbind • 63 views
ADD COMMENTlink modified 10 weeks ago by Rory Stark2.9k • written 10 weeks ago by danielaperry20150
Answer: diffBind analysis: only one replicate
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gravatar for Rory Stark
10 weeks ago by
Rory Stark2.9k
CRUK, Cambridge, UK
Rory Stark2.9k wrote:

Actually, you have no replicates for this TF, only a single sample. Which could be an outlier, you have no way of knowing without replication.

Without replicates you can not do any meaningful statistical analysis. You can do things like look at peak overlaps with other factors, or look at relative enrichment in this sample compared to other peaks identified as being differentially bound. But you can't identify differentially bound peaks for this factor with any confidence.

ADD COMMENTlink written 10 weeks ago by Rory Stark2.9k
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