Hi, I have the raw proteomics data and I am doing differential analysis using DEqMS.

I am using two variables to create a group

groups<factor(paste(final_val_C$Qp_Group,final_val_C$Day,sep='.'))

The day is numeric and Qp_Group consists of "high" and "low variables and Days consist of 3,5,8 and 11 days

My group combination looks like this

high.3 high.5 high.8 high.11 high.3 high.5 high.8 high.11 high.3 high.5 high.8 high.11 high.3 high.5 high.8 high.11 high.3 high.5 high.8 high.11 high.3 high.5 high.8 high.11 low.3 low.5 low.8 low.11 low.3 low.5
low.8 low.11 low.3 low.5 low.8 low.11 low.3 low.5 low.8 low.11 low.3 low.5 low.8 low.11 low.3 low.5 low.8 low.3 low.5 low.8
low.11 low.3 low.5 low.8 low.11 low.3 low.5 low.8 low.11
Levels: high.11 high.3 high.5 high.8 low.11 low.3 low.5 low.8

design = model.matrix(~0+groups)
colnames(design) = gsub("groups","",colnames(design))
fit1 <- lmFit(log2(proteomeRaw), design)
fit3 <- eBayes(fit1)
EqMS.results = outputResult(fit3)

I am not using contrasts as I don't have any separate ones to compare. My outputResult function is throwing this error even when I use Day as char.

"Error in `$<-.data.frame`(`*tmp*`, "sca.adj.pval", value = numeric(0)) : replacement has 0 rows, data has 8183"

Any idea