Question: no replicates data
0
gravatar for yueli7
12 months ago by
yueli70
China
yueli70 wrote:

Hello,

 

I have no replicated human cancer cell data, and trying to use edgeR.

 

In the user's guide "edgeR: differential expression analysis of digital gene expression data",

2.1.1 What to do if you have no replicates

2. Simply pick a reasonable dispersion value.

 

What of the bcv value is suitable for human cancer cell, 0.4,0.1 or 0.01?

 

Thanks in advance?


 

edger • 221 views
ADD COMMENTlink modified 12 months ago by Gordon Smyth37k • written 12 months ago by yueli70
Answer: no replicates data
2
gravatar for Aaron Lun
12 months ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

You don't provide a lot of context. But if the data are from a human cancer cell line, generated under tightly controlled conditions in a laboratory environment, you could expect dispersions below 0.01 (i.e., BCVs < 0.1) to be "reasonable". On the other hand, if the data are from actual patients, you can expect BCVs at or above 0.5 - see the Nigerian case study (Section 4.3) in the edgeR user's guide.

Obviously, these are just very general observations. No pre-defined "reasonable" dispersion value is a good substitute for actually having replicates in your experiment.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Aaron Lun23k

Thank you so much for your great help!
 

ADD REPLYlink written 12 months ago by yueli70
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