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NA is p-valueas & p.adj in DESeq2

Already Answered: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na

HI, I am doing DE analysis using DESEq2. I obtained the lists of DEGenes, however there are genes that do not show any p.values. Additionally there are genes that have p.values but do not have p.adjusted values (=NA).

I do not really iunderstand how mathematically it can happen, how can I not have a p.values AND how can I have a p.value but not have a p.adj. Would really appreciate if someone explains me.

Thanks for the help in advance!

Here follows the summary of my list:

summary(as.data.frame(dds_Xl))

     log2FoldChange                    
**Min**.   :-20.965658 
**1st Qu.**: -0.034033   
**Median**:  0.000681     
**Mean**: -0.004753       
**3rd Qu.**:  0.037401     
**Max. ** :  3.504429   

       pvalue      
 Min.   :0.0000 
1st Qu.:0.1242   
 Median :0.3765  
Mean   :0.4114   
3rd Qu.:0.6756  
Max.   :0.9999   
 NA's   :54     

     padj      
Min.   :0.000  
1st Qu.:0.427  
Median :0.695  
Mean   :0.633  
3rd Qu.:0.873  
Max.   :1.000  
NA's   :3496
fdr deg p-value deseq2
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written by Milly • Milly

1 answer

Please read the manual first, it's a FAQ: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na

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written by ATpoint ATpoint

Thank you very much! I somehow missed that part.

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written by Milly • Milly

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