Question: Why are lowly expressed genes less likely to detect as DE?
gravatar for statfa
4 months ago by
statfa450 wrote:


In my study, I have realized that the model I use is not able to detect DE genes if genes are lowly expressed. What can be th reason that lowly expressed genes are less likely to be detected as DE even if they are truely DE?

I am not talking about increasing the power of analysis by removing lowly expressed genes as they may be affected by noises. I am talking about the situation in which my lowly expressed genes are important but my model cannot detect differences in expressions. why is that?

Thank you

rna-seq de • 164 views
ADD COMMENTlink modified 4 months ago by Devon Ryan91k • written 4 months ago by statfa450
gravatar for Devon Ryan
4 months ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

The strength of fold change and variance shrinkage scales inversely with the size of the values (and the number of them). As a rule, power increases with sample number and the number of read counts per gene.

ADD COMMENTlink written 4 months ago by Devon Ryan91k

Thank you. Do you have any reference for this, please?

ADD REPLYlink written 4 months ago by statfa450

I found the reference here. Thank you

ADD REPLYlink modified 4 months ago • written 4 months ago by statfa450
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