Hello,
When running DESeq, we get some genes with p-values that are NA (See below). They're probably supposed to be zero or really close to zero. How can we fix this?
happygrad:~/work/kristen/DEseqTroubleshooting> head -n 1 DE_genes_Reps6_allres.txt
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj adjLog2FoldChange
happygrad:~/work/kristen/DEseqTroubleshooting> grep NA DE_genes_Reps6_allres.txt
NM_001012669 13245.90643904 1967.80257160171 24524.0103064784 12.4626375940331 3.63953752770609 NA NA 3.63886339029247
NM_001024569 1861.17241176578 0.626705575521935 3721.71811795603 5938.54317453056 12.5358933415034 NA NA 11.1601875099376
NM_001034039 5972.12221805081 11639.9873990581 304.257037043527 0.0261389490050605 -5.25765505536172 NA NA -5.2530450700836
We're running version 2.15.0
Platform = x86_64-pc-linux-gnu (64 bit)
These are the commands we're using:
cds <- newCountDataSet(countsTable, cond)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
res <- nbinomTest(cds, "1", "2")
Thanks,
Danielle
When running DESeq, we get some genes with p-values that are NA (See below). They're probably supposed to be zero or really close to zero. How can we fix this?
happygrad:~/work/kristen/DEseqTroubleshooting> head -n 1 DE_genes_Reps6_allres.txt
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj adjLog2FoldChange
happygrad:~/work/kristen/DEseqTroubleshooting> grep NA DE_genes_Reps6_allres.txt
NM_001012669 13245.90643904 1967.80257160171 24524.0103064784 12.4626375940331 3.63953752770609 NA NA 3.63886339029247
NM_001024569 1861.17241176578 0.626705575521935 3721.71811795603 5938.54317453056 12.5358933415034 NA NA 11.1601875099376
NM_001034039 5972.12221805081 11639.9873990581 304.257037043527 0.0261389490050605 -5.25765505536172 NA NA -5.2530450700836
We're running version 2.15.0
Platform = x86_64-pc-linux-gnu (64 bit)
These are the commands we're using:
cds <- newCountDataSet(countsTable, cond)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
res <- nbinomTest(cds, "1", "2")
Thanks,
Danielle
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