Question: ChickPea DEG Analysis
0
gravatar for deepkumar1983
4.0 years ago by
United States
deepkumar198340 wrote:

Hi,

I have chickpea  rnaseq data of control vs treated without any replicate. I had used HTseqCount for count the gene and want to use edgeR for identifying DEG. My question is what should be the ideal value for dispersion parameter because it was mentioned in edgeR manual that for  well-controlled experiments are 0.4 for human data, 0.1 for data on genetically identical model organisms or 0.01 for technical replicates.
Any help will be appreciated.

 

Thanks

Dr. Deepak


 

edger • 1.1k views
ADD COMMENTlink modified 4.0 years ago by PoGibas4.8k • written 4.0 years ago by deepkumar198340

Dispersion will be estimated from your data. You don't need to specify any value in edgeR. This gives an idea about the variation in your data across replicates.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by geek_y9.8k

Thanks for the reply. But i have no replicates.
 

ADD REPLYlink written 4.0 years ago by deepkumar198340

You could use DESeq. It tries to estimate dispersion without replicates.

ADD REPLYlink written 4.0 years ago by geek_y9.8k
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