Question: about dispersion_plot and dispersion_plotLocal in DEseq2 analysis
gravatar for Emily
4.8 years ago by
United States
Emily0 wrote:

Hi everyone,

I am a starter in the RNAseq data analysis, I really have some questions about the DEseq analysis. After running the DEseq in R, I got several files, two of them is diffgene_results.csv and diffgene_resultsLocalFit.csv, which file should I use to get the differentially expressed genes? And I also found that in all my cases, diffgene_resultsLocalFit.csv has more differentially expressed genes than in  diffgene_results.csv . Should I based on the dispersion plot and dispersion Localplot to decide which file should I use? Or I should use the file which gives me more differentially expressed genes?  Thank you very much in advance.


sequencing rna-seq next-gen • 1.1k views
ADD COMMENTlink modified 4.8 years ago by Devon Ryan91k • written 4.8 years ago by Emily0
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

I'm guessing that you're using a galaxy workflow that someone else made rather than actually running DESeq (I hope you mean DESeq2) yourself.

In any case, I would normally use the parametric fit results (diffgene_results.csv) unless you received a warning during the fitting or can see in the plot that it fits poorly. Don't just blindly use the one that gives more DE results...that's a good way to waste large amounts of time and money.

ADD COMMENTlink written 4.8 years ago by Devon Ryan91k

Hi Devon,

Thank you very much for your help. Yes, I mean DEseq2. When I ran DEseq2, I do get some warning like NAs produced. But the parametric fit is not poor. The following is the parametric and local fit plot, so I should use the parametric fit right?

I appreciate your help.




ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Emily0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2326 users visited in the last hour