Question: Too many DEGs
gravatar for Raymond
4 months ago by
Raymond0 wrote:

Hi, I have 36 animals and got two tissues of each animal for RNAseq.

My design model is: sample+tissue

and I got DEG results like that:

out of 16445 with nonzero total read count adjusted p-value < 0.05 LFC > 0 (up) : 7276, 44% LFC < 0 (down) : 7508, 46% outliers [1] : 0, 0% low counts [2] : 0, 0% (mean count < 4)

90% of genes are DEGs at the level of 0.05. Is there any problem with my results?

Below I attached two figures:

1.Normalization figure. I plot the density function of the gene vst expressions in each sample. The figures showed that two tissues are different, but all normalized to the median.


  1. Gene expression data. I rank the average gene expression of genes in Tissue1, and the then plot all genes in Tissue2 based on the ranking order in Tissue1.


From this figure, it seems that a lot of genes between these two tissues are quite close to each other, there should not be so many DEGs.

Any suggestions?

Thanks for your time & regards,


deseq2 • 102 views
ADD COMMENTlink modified 4 months ago by Michael Love25k • written 4 months ago by Raymond0

Can you edit this post and show the code you used for the analysis?

ADD REPLYlink written 4 months ago by Steve Lianoglou12k
Answer: Too many DEGs
gravatar for Michael Love
4 months ago by
Michael Love25k
United States
Michael Love25k wrote:

You are testing a point null and have many samples. We discuss this situation in the DESeq2 paper. Why not specify an LFC threshold?

ADD COMMENTlink written 4 months ago by Michael Love25k
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