Question: Histogram of p values for all tests
gravatar for shivyasoni1994
19 months ago by
shivyasoni19940 wrote:

Hi, I am trying to do differential-gene-expression analysis with DESeq2, for that i have done pseudo-alignment using Salmon , and with tximport, gene-level abundance is calculated. I am following "Analyzing RNA-seq data with DESeq2", tutorial. I got Histogram of p values for all tests.

enter image description here

Please, guide me to interpret this plot. Can I proceed with the data, (for heatmap generation), showing above plot.

Thanks in advance!

rna-seq deseq2 • 1.3k views
ADD COMMENTlink modified 18 months ago by tw61740 • written 19 months ago by shivyasoni19940

Correct what? Please specify.

ADD REPLYlink written 19 months ago by ATpoint34k
gravatar for Nicolas Rosewick
18 months ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

Start reading this excellent article here :

These two peaks at the right tail are strange. Did you use the nominal pvalue or the corrected one (you should use the nominal for the plot) ?

Otherwise the distribution seems to be anti conservative so it's good 😉

ADD COMMENTlink written 18 months ago by Nicolas Rosewick8.8k
gravatar for tw617
18 months ago by
tw61740 wrote:

The two main patterns you should look for when interpreting p-value histograms are: a sharp spike near 0 ( like you have here) that drops off into a somewhat uniform distribution. This indicates that you have some significant differences. The other pattern would be a totally uniform (flat) distribution, this indicates no significant difference. Here it looks like you have the first and ideal pattern although those spikes near one are a bit weird. I think they are probably errors/genes with no or little reads that were not filtered out. Usually you should exclude genes with less than 10 total reads.

ADD COMMENTlink written 18 months ago by tw61740
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