Question: why two packages have not similar FDR ???
gravatar for unique379
4.9 years ago by
unique37990 wrote:

Hello folks, I am wondering why deseq2 and edgeR results are not agreed to each in terms of FDR while both calculated almost same LogFC and Nominal/Raw p-values ?? It seems DESeq2 has more stringent view to compute the FDR and control the genes than edgeR. I ran analysis with the same initial filtering applied in edgeR and further used the same filtered data for DESeq2 with cooksCutoff=F, independentFiltering=FALSE in results function.

Parameters Used in both methods are:

rowSums(cpm(data)>1) >= ncol(data)/2

Sample = 6; each have 3 replicates ; group = C and T

adjust.method = "BH"

Dispersion , Model fit and testing in both methods applied = GLM and LRT

In particular for edgR:

y <- estimateGLMCommonDisp(y,design)

y <- estimateGLMTrendedDisp(y,design)

y <- estimateGLMTagwiseDisp(y,design)

fit <- glmFit(y,design)

lrt <- glmLRT(fit,coef=2)

In particular for DEseq2:

ddsLRT <- DESeq(dds, test ="LRT", reduced = ~1)

resLRT <- results(ddsLRT, cooksCutoff=F, independentFiltering = F)


No. of DE genes detected in edgeR ( Raw p-value <= 0.05) = 16 # I am only showing here 9 genes/miRNAs.

No. of DE genes detected in edgeR ( FDR <= 0.05) = 8

No. of DE genes detected in edgeR ( FDR <= 0.05) = 4

Note: Basically i am wondering about last 5 genes/miRNAs. Any clue ??

Results from edgeR and DESeq2

edger rna-seq deseq mirnaseq R • 1.7k views
ADD COMMENTlink modified 4.9 years ago by Devon Ryan98k • written 4.9 years ago by unique37990
gravatar for Devon Ryan
4.9 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

They use the exact same function to compute the adjusted p-value. Since this is dependent on the distribution of p-values and the p-values themselves are slightly different, this sort of result is typical.

ADD COMMENTlink written 4.9 years ago by Devon Ryan98k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2348 users visited in the last hour