Question: How to find significantly stably expressed miRNA with DESeq2 DE results
1
gravatar for mariakarand
3.8 years ago by
mariakarand10
Norway
mariakarand10 wrote:

Hi,

I'm working with DESeq2 DE results of microRNA expression (which I have not myself performed). I want to identify both differentially expressed miRNA and significantly stably expresssed miRNA. The DE miRNAs are obviously the miRNA with p<0.05. How can I identify stably expressed miRNAs from the DESeq2 DE resaults? Is there any specific p-value threshold I can use (e.g all miRNA with baseMean over 10 and a p-value over 0.5 can be viewed as significantly stably expressed)?

Just to clearify, I'm not looking for stably expressed miRNAs to normalize the data, but rather to identify which miRNAs are DE, which miRNA are significantly stably expressed and which are neither.

-Maria

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by mariakarand10
Answer: How to find significantly stably expressed miRNA with DESeq2 DE results
1
gravatar for Sean Davis
3.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

I wrote a blog post summarizing some email exchanges on this subject.

http://watson.nci.nih.gov/~sdavis/blog/testing-for-non-differentially-expressed-genes/

 

ADD COMMENTlink written 3.8 years ago by Sean Davis21k

Thanks!

A follow-up question: Is there any key to find what threshold you should use, or do you generally recomend a treshold -value of abs(0.3)?

And in the R-script it's first written

theta <- .3

But the "theta" is never used again, rather "thr" is used in the Z-tests. Is this a typo? Is "thr" really "theta"?

Maria

ADD REPLYlink written 3.8 years ago by mariakarand10
Answer: How to find significantly stably expressed miRNA with DESeq2 DE results
1
gravatar for Michael Love
3.8 years ago by
Michael Love24k
United States
Michael Love24k wrote:

DESeq2 has built in functionality for testing for effects such that |beta| < T for some threshold T.

see the lfcThreshold and altHypothesis arguments in ?results.

There is a diagram in the vignette showing this, and a Figure in the DESeq2  paper showing an MA plot for a test of |beta| < T

http://www.genomebiology.com/2014/15/12/550/figure/F4

ADD COMMENTlink written 3.8 years ago by Michael Love24k
Answer: How to find significantly stably expressed miRNA with DESeq2 DE results
0
gravatar for mariakarand
3.8 years ago by
mariakarand10
Norway
mariakarand10 wrote:

Thanks!

A follow-up question: Is there any key to find what threshold you should use, or do you generally recomend a treshold -value of abs(0.3)?

And in the R-script it's first written

theta <- .3

But the "theta" is never used again, rather "thr" is used in the Z-tests. Is this a typo? Is "thr" really "theta"?

Maria

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by mariakarand10
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