no H cmponenet after running the "zlm" function

[kristinazuza]

Hi,
I have been running MAST on scRNAdata set, containing 96 samples.
After running the zlm on sca object, I run summary, and only get coefficient "c", "D", "S" and "logFC" but no "H" coefficient. I am not sure why is that and was wondering if you could help me with it or give some input.
Here is the code I run:

sca <- SceToSingleCellAssay(sce = sce, class = "SingleCellAssay", check_sanity = FALSE)

cdr2 <-colSums(assay(sca)>0)
colData(sca)$cngeneson <- scale(cdr2)
colnames(colData(sca))

cond <- factor(colData(sca)$category)
cond<-relevel(cond,"NR")
colData(sca)$condition<-cond
cond
zlmCond <- zlm(~ cond + cngeneson,  sca)


summaryCond <- MAST::summary(zlmCond)
summaryDt <- summaryCond$datatable


print(summaryCond, n=4, by='D')
print(summaryCond, n=4, by='C')
print(summaryCond, n=4, by='S')


fcHurdle <- merge(summaryDt[contrast =='condall3' & component=='H', .(primerid, 'Pr(>Chisq)' )] , summaryDt[contrast=='condall3' & component=='logFC', .(primerid, coef, ci.hi, ci.lo)], by='primerid') 

fcHurdle[,fdr:=p.adjust('Pr(>Chisq)', 'fdr')]

Hope you will have time to check it and give some input.
Thank you in advance.

Regards,
Kristina

[gfinak]

Where does the data for sce come from?

[kristinazuza]

Hi,

it comes fromscater and normalize function.

[gfinak]

That's great. But I can't reproduce your issue without some data.
Please see the reprex package for how to build a minimal reproducible example, and provide some minimal data to reproduce your error so that I can investigate it.