Hi, I have a proteomics data set and I am doing the differential analysis on that. I used the Limma package to do that. I first removed the negative counts and did the analysis but I am getting all upregulated ones and none of the ones are down .
groups<-interaction(final_val_C144$Qp_Group,final_val_C144$Day)
design = model.matrix(~0+groups)
colnames(design) = gsub("groups","",colnames(design))
d0 <- DGEList(proteomeRaw_c144)
d0 <- calcNormFactors(d0)
y<-voom(d0,design,plot=T)
fit <- lmFit(y, design)
head(coef(fit))
fit1 <- eBayes(fit)
top.table <- topTable(fit1, sort.by = "F", n = Inf)
On running the below code, I get the following output
summary(decideTests(fit1))
Down 0 0 0 0 0 0 0 0
NotSig 0 0 0 0 0 0 0 0
Up 8106 8106 8106 8106 8106 8106 8106 8106
Any help .
Cross-posted to Bioconductor https://support.bioconductor.org/p/9142067/
@OP, can you please stop crossposting to that extend? It splits information across multiple communities and doubles the effort for users. Please consider to decide for one community and then wait whether you get answers in a reasonable timespan (a few hours is not "reasonable", rather days).