fit.bystim <- zlm.SingleCellAssay(~cngeneson+Stim/Time,sca=filtered_nobaseline,method="ridge",ebayes=TRUE,hook=deviance_residuals_hook,lambda=0.1)
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.
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")
)))
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2