mDC Cell Maturation

Fit zlm to stimulation and timepoint

fit.bystim <- zlm.SingleCellAssay(~cngeneson+Stim/Time,sca=filtered_nobaseline,method="ridge",ebayes=TRUE,hook=deviance_residuals_hook,lambda=0.1)

Test for any time effect in LPS

In the LPS stimulation, testing for any time effect, when adjusting for ngeneson we detect 1359 differentially expressed genes. When we don’t adjust for ngeneson, we detect 1996 genes.

Gene set enrichment analysis

cache(boot_shalek <- bootVcov1(zlmfit = fit,R = 100))
cache(gsea.time <-
lapply(hyp,function(x)
gseaAfterBoot(
fit,boot_shalek,sets,hypothesis = x,control = list(n_randomize = Inf,var_estimate = "bootall")
)))

PIC Stimulation GSEA

PAM Stimulation GSEA

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LPS Stimulation GSEA

Residuals within significant modules

PCA of core antiviral residuals

Module scores

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Visualization of residual correlation over time in LPS

Correlations accounting for ngeneson

PC plot of residuals in LPS

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Fit PAM and PIC

Visualization of residual correlation over time in PAM

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Visualization of residual correlation over time in PIC

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