DESeq2 rlog output some genes all zero value.
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4.0 years ago
MatthewP ★ 1.4k

Hello, here is normalized counts and rlog values from same dds for one gene as an example.
counts(dds, normalized=TRUE)

$grep ENSG00000285390 NormalizedReadCounts.csv
ENSG00000285390,93974,ATP5IF1,ATP synthase inhibitory factor subunit 1 [Source:HGNC Symbol;Acc:HGNC:871],0,152.9196357348574,0,0,140.25796849320326,0,0,0,0,0,0,0,0,0,0,0,0,137.84888273256348,0,0,0

assay(rlog(dds, blind = FALSE))

$grep ENSG00000285390 RlogNotBlind.csv                                                                                                                                                       
ENSG00000285390,93974,ATP5IF1,ATP synthase inhibitory factor subunit 1 [Source:HGNC Symbol;Acc:HGNC:871],0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

assay(rlog(dds), blind = TRUE) $grep ENSG00000285390 RlogBlind.csv

ENSG00000285390,93974,ATP5IF1,ATP synthase inhibitory factor subunit 1 [Source:HGNC Symbol;Acc:HGNC:871],0.3768414649020013,7.444652197992587,0.34193122192703185,0.3422759766396466,8.061531802720873,0.3412463595404267,0.3453624248405609,0.33763408016003904,0.9417870115160176,0.7274532822427769,0.4651761278955451,0.4315289608138566,0.4326192274258369,3.251728989194549,0.3782770162572964,0.3846700100916518,0.3402193431192049,9.503699082053876,0.3449460628281691,0.373096194492067,0.38414746774517305

Why blind = FALSE comes out all zero value?

RNA-Seq DESeq2 • 679 views
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