deseq2 low read input
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Bob • 0
@bob-12005
Last seen 5.4 years ago

Hi all 

for prevent p-values set to NA in DESeq2, should I offset my raw reads as same as this ?

Thanks

      cont1  cont2 cont3 tumor1 tumor2 tumor3
geneA    64     80    36      0      0      0
geneB    66     87    56      1      0      0
deseq2 • 706 views
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What do you mean by "offset"?

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replace 0 with 1 and add 1 to each control reads for instance change the raw reads to :

  cont1  cont2 cont3 tumor1 tumor2 tumor3
geneA    65     81    37      1      1      1
geneB    66     88    57      1      1      1

 

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@mikelove
Last seen 10 hours ago
United States

No you should not ever alter the counts for DESeq2. If you want to stop p-values being set to NA, see this section:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#how-can-i-get-unfiltered-deseq2-results

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for gene A  the basemean is 0 so p-value adjusted to NA  and this gene shows dysregulation in tumor samples if I exclude some genes as same as this from count matrix I will have false positive/negative result, is it true?

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Base mean of 0 means the experiment had no observations of the gene (according to how you are quantifying). DESeq2 can’t help you measure DE for a gene with no observations obviously.

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