Question: about dispersion_plot and dispersion_plotLocal in DEseq2 analysis
0
gravatar for Emily
4.3 years ago by
Emily0
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 4.3 years ago by Devon Ryan88k • written 4.3 years ago by Emily0
0
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k 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 4.3 years ago by Devon Ryan88k

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.

Emily

 

 

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Emily0
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