edgeR analysis outputs FDR equals 1
Hello, people!
I have found different answers for similar questions but none of them fits with my case. I am using edgeR to do the statistics of my RNAseq data and, as shown bellow, I have 3 replicates for each of two groups:
> x <- read.delim("youngxsenes_comparison_table.csv",row.names="miRNAs")
> group <- factor(c(1,1,1,2,2,2))
> y <- DGEList(counts=x,group=group)
> y <- calcNormFactors(y)
> design <- model.matrix(~group)
> y <- estimateDisp(y,design)
> et <- exactTest(y)
> topTags(et)
logFC logCPM PValue FDR
hsa-mir-3613 0.9061035 8.5155819 0.001912410 1
hsa-mir-6825 2.3963572 -1.6642635 0.001941057 1
hsa-mir-133a-1 -3.3808103 1.9433720 0.002665153 1
hsa-mir-133a-2 -3.0362991 3.3413262 0.003145797 1
hsa-mir-5008 1.9878428 -0.7387409 0.003295906 1
hsa-mir-214 -0.6672389 11.3911591 0.005099100 1
hsa-mir-124-1 1.3643040 1.5929070 0.005458540 1
hsa-mir-124-3 1.2313130 2.6963757 0.005794421 1
hsa-mir-203a -2.1373892 2.5981025 0.005921462 1
hsa-mir-522 -2.7536418 -1.9466949 0.006955708 1
Even though my data have 3 replicates, FDR remains equal 1. I read this is common for data with no replicates. Does anynone know why this also happens in my case?
Thank you
1 answer
The link below might explain it...see how a p-value of 0.05 isn't good enough when you have 20 tests? If you have a 500 genes, a p-value of 0.002 isn't good enough. You might really have no real changes, or those changes might be too subtle to show with only three replicates.
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