Question: Disproportionate Amount of Up-regulated Genes
gravatar for Stoploss25
5.3 years ago by
United States
Stoploss2510 wrote:

Hi, we did an RNA seq experiment recently. It was 3 replicates for 2 conditions. One replicate turned out to be contaminated so I have eliminated it. I want to do differential expression analysis.


I have a script for EdgeR and it works fine, however I am getting way too many upregulated genes. When I do a summary EdgeR tells me there are 83 upregulated genes, 13 downregulated. This does not really make sense and there is nothing about either of these two conditions that should cause  a large activation / deactivation of transcription. Im wondering what I can do to correct this. How do I go about diagnosing if theres anything wrong with my replicates and what can be done to correct for it.


I think the dispersion was a little high Disp = 0.10443 , BCV = 0.3232. Ive tried fiddling with the counts per million cutoff and it helps a bit but Im wondering if I can do anything else


targets <- readTargets()
x <- read.delim("EdgeR.counts.m.txt", row.names=1, stringsAsFactors=FALSE)
y <- DGEList(counts=x[,1:5], group=targets$Treatment)
colnames(y) <- targets$Label
keep <- rowSums(cpm(y)>5) >= 3
y <- y[keep,]
y$samples$lib.size <- colSums(y$counts)
y <- calcNormFactors(y)
y <- estimateCommonDisp(y, verbose=TRUE)
y <- estimateTagwiseDisp(y)
wm <- exactTest(y, pair=c("wt","mt"))
summary(de <- decideTestsDGE(wm))
top <- topTags(wm)
ADD COMMENTlink modified 5.3 years ago by Devon Ryan98k • written 5.3 years ago by Stoploss2510
gravatar for karl.stamm
5.3 years ago by
United States
karl.stamm3.9k wrote:

You think 83 genes is a lot?  How many are in the counts table? Human's got about 20-30 thousand. You'd expect more than 83 by random noise. 

ADD COMMENTlink written 5.3 years ago by karl.stamm3.9k

Yes I do think 83 >> 13. You are disagreeing with this?. Even if it was 'random noise' you would expect it to be equal, if there was nothing else going on. 

ADD REPLYlink written 5.3 years ago by Stoploss2510

Oh I misunderstood. You're concerned with the imbalance. I don't think it's a problem, but I also don't have a good justification for you.  Possibly one pathway is activated and another deactivated, and one happens to carry 83 genes, the other 13. You're sensitive to our definitions and discoveries of gene IDs. 

ADD REPLYlink written 5.3 years ago by karl.stamm3.9k
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:
  1. Just because there's no a priori reason to expect an imbalance in up/down regulated genes doesn't mean there won't be one.
  2. Try doing some independent filtering with the genefilter package. That'll let you maximize the number of DE genes. Since you mentioned that increasing cutoffs decreases the imbalance it could simply be that you're better able to measure upregulated vs. downregulated the p-values for the downregulated genes could just be a bit deflated from what they might otherwise be.
ADD COMMENTlink written 5.3 years ago by Devon Ryan98k

Thanks will look into this

ADD REPLYlink written 5.3 years ago by Stoploss2510
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