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Question of Padj value (very high, infinite) got from dds

Bioinformatics Asked on May 10, 2021

After I got dds from my count matrix by DESeq(), I use results() method to get Padj and log2 fold changes for volcano plotting,
then I found some gene’s Padj values are infinite and the P-value is very close to 0;
this makes those dots on my volcano plotting located very top to Y-aix and also confused me:

  1. is this normal or not, such a p-value (very close to 0) and -logPadj is infinite;
  2. how should I treat those data: are they very different expressed between samples and control or just abnormal data which should be taken off?

Here follows the table:
enter image description here

table 1 is dds results, -log10(padj) show inf;
table 2 is count matrix from featureCount
table 3 is size factor of samples

Please help me !

One Answer

  1. The fold changes for those are huge (on the order of 32x for the largest), so it's unsurprising for the adjusted p-values to be absurdly small.
  2. There's no reason to treat them differently.

Correct answer by Devon Ryan on May 10, 2021

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