[BioC] DESeq and EdgeR log fold differences

[Ioannis Vlachos]

Hello everyone,

I thought of conducting a parallel DE analysis with EdgeR and DESeq using a
dataset that I have been working on lately.

The dataset has two conditions with two biological replicates each.

Let's say: Wild Type, Wild Type, Knock Out, Knock Out.

It's a smallRNA-Seq dataset, mapped to miRNAs.

I have tried various analyses using both programs and I have noticed this.

There are very large differences in fold changes for some miRNAs between the
two programs, even when using "RLE" for EdgeR normalization.

Example:

DESeq Code:

countDataSet = newCountDataSet (DATA, condition)   
countDataSet = estimateSizeFactors(countDataSet)
 countDataSet = estimateDispersions(countDataSet)  
 difexp = nbinomTest (countDataSet, "WildType", "KnockOut")

one of the results is:

id	baseMean	baseMeanA	baseMeanB	foldChange
log2FoldChange	pval	padj
100	623.8597966	349.3576527	898.3619406	2.57146776
1.362592066	0.001303353	0.182310802

And the size factors for DESeq are:


sizeFactors(countDataSet)

      KO1       KO2       WT1       WT2 
1.2969960 1.052 0.8850 0.84442


OK. So far so good.

EdgeR now.

dge <- DGEList(counts=DATA, group=condition)
dge<- calcNormFactors(dge)
dge <- estimateCommonDisp(dge, verbose=TRUE)
dge <-estimateTagwiseDisp(dge, verbose=TRUE)
et<- exactTest(dge)

Which results in:
	logFC	logCPM	PValue		FDR
100	-2.750	5.814103	9.40E-09	1.20E-05

With:
dge$samples
    group lib.size norm.factors
WT1     1  2796302    0.9922204
WT2     1  2610244    0.9928183
KO1     2  3999488    1.0248098
KO2     2  3349646    0.9905555

We have logFC 1.3 for DESeq and 2.75 in EdgeR

And these results remain practically the same even by using:

dge<- calcNormFactors(dge.RLE, method="RLE")

                     logFC    logCPM       PValue          FDR
210    -2.775952  5.823856 8.047631e-09 1.030902e-05

       group lib.size norm.factors
KnockOut  3999488    1.0147156
KnockOut  3349646    0.9830163
WildType  2796302    0.9903844
WildType  2610244    1.0122579


Any thoughts?

This entry has (raw tags):
KO	KO	WT	WT	
 131	123	287	195

Any thoughts on why I get 1.3 lFC vs 2.7lFC?

Thanks a lot,

Best Regards,

Ioannis