Hi,

I am working on a treatment's bulk RNA-seq of responders and non-responders(5 responders,4 non-responders). P adjusted values are 1 when tried with the Wilcox test in Seurat, presto packages. But in Deseq2 and EdgeR(T-Test), there are significant FDR values. I have tried with FPKM values after normalization.

Thanks in advance.

Here is the code I used:

pvalues <- sapply(1:nrow(count_norm),function(i){                                                                                                
             data<-cbind.data.frame(gene=as.numeric(t(count_norm[i,])),conditions)                                                        
             p=wilcox.test(gene ~ conditions, data)$p.value                                                                                    
             return(p)                                                                                                                                                          
})

fdr=p.adjust(pvalues,method = "BH")