Question: Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
0
gravatar for juls
2.5 years ago by
juls0
juls0 wrote:

Dear all,

I am using the cor.test function (Spearman/Pearson correlation) to find coexpressed genes for a specific gene of interest in my microarray dataset (226 samples).

My question is now - what is the established cutoff for coexpression? Just the p-value results in a large number of coexpressed genes. I also categorised the genes according to correlation coefficient as in this list (see below), but is there any established cutoff > 0.5 or is indeed mainly the p-value used?
 

0-0.19 very weak
0.20-0.39 weak
0.40-0.59 moderate
0.60-0.79 strong
0.80-1.0 very strong

Thanks for advice!

Julia 

 

 

 
 

 

 

 

 

ADD COMMENTlink modified 2.5 years ago by James W. MacDonald50k • written 2.5 years ago by juls0
Answer: Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
0
gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald50k wrote:

What about negative correlation? Is that not co-expression of a type as well?

Anyway, I am not sure inference will help you here, as a p-value doesn't measure the strength of correlation. Instead it just says how likely your result would be if the two genes really were not correlated. With 226 samples, even a pretty small correlation will have a p < 0.05 (somewhere around 0.11 or so). You will probably just have to set some ad hoc cutoff that you define as 'correlated enough' and go with that.

ADD COMMENTlink written 2.5 years ago by James W. MacDonald50k

Thanks for your answer.

I adjusted the p value, so it's around 0.18 but yes it's very low. Hence my question about an "established" cutoff. Any suggestions about a sensible cutoff here?
(The above list was also meant for negative correlation of course. I classified with the abs(correlation). I thought that was clear ;) - sorry)

 

ADD REPLYlink written 2.5 years ago by juls0
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