Table 2 Comparisons of DESeq2 results using current study parametersa vs. parameters recommended for increasing true positives through zero-inflation handlingb, for selected differential expression analyses (DEAs)

From: Transcriptional impacts of substance use disorder and HIV on human ventral midbrain neurons and microglia

Cell type

DEA

N up DEGs reported in our paper

N up DEGs common to both approaches

N down DEGs reported in our paper

N down DEGs common to both approaches

Dopaminergic neuron

SUD+HIV− vs. SUD−HIV−

0

0

51

49

Dopaminergic neuron

SUD+HIV+u vs. SUD−HIV+u

82

76

41

41

Dopaminergic neuron

SUD+HIV+d vs. SUD−HIV+d

0

0

0

0

  1. aWald test, useT = False, default sizeFactors, and pseudocount addition.
  2. bLikelihood ratio test, useT = True, minmu = 1e-6, sizeFactors from scran::computeSumFactors, and no pseudocount addition.
  3. DEG: Differentially expressed gene.
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