**10**wrote:

Hi,

I have done differential expression on same date with both of DESeq2 and EdgeR but I am seeing contradict results. For instance DCK6 shows positive 1 fold change by DESeq2 while -1 fold change by EdgeR. I really got confused which one is right?

```
condition = as.factor(c(rep ("TRG1-2",26), rep("TRG4-5", 30)))
mycols = data.frame(row.names = c("A2", "A3", "A4", "A6", "A7", "A8", "A9", "A10", "A11", "A12", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11", "B12", "C1", "C2", "C3", "C4", "C5", "C6", "G12", "D1", "D2", "D3", "D4", "D5", "D6", "D7", "D8", "D9", "D10", "D11", "D12", "E1", "E2", "E3", "E4", "E5", "E6", "E7", "E8", "E9", "E10", "E11", "E12", "F1", "F2", "F5", "F6", "F7", "G8"))
mycols$condition= c("TRG1-2","TRG1-2", "TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG1-2","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5","TRG4-5", "TRG4-5")
dds=DESeqDataSetFromMatrix(countData = df, colData = mycols, design = ~ condition)
dds <- DESeq(dds)
DESeq2 <-results (dds, contrast=c("condition", "TRG1-2", "TRG4-5"))
> head(DESeq2)
baseMean log2FoldChange lfcSE stat pvalue padj
CDK6 1617.5983 1.667070 0.2901847 5.744858 0.0000000092 0.0000202
CALML5 378.1458 1.496815 0.4058617 3.687992 0.0002260310 0.0653134
KLK5 1540.0631 1.472039 0.4948118 2.974946 0.0029304000 0.1895279
KRT14 22457.5507 1.337578 0.6644294 2.013122 0.0441017650 0.4903814
KRT17 9115.3139 1.182890 0.5461288 2.165954 0.0303146840 0.4473959
S100A7A 351.9248 1.049479 0.3290714 3.189213 0.0014266070 0.1329832
```

For EdgeR

```
> group = condition
> group
[1] TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2
[17] TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG1-2 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5
[33] TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5
[49] TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5 TRG4-5
Levels: TRG1-2 TRG4-5
> dim(df)
[1] 2560 56
> y <- DGEList(counts = df, group = condition)
> y <- estimateDisp(y)
Design matrix not provided. Switch to the classic mode.
> sqrt(y$common.dispersion)
[1] 0.6280918
> EdgeR <- exactTest(y)
> topTags(EdgeR)
Comparison of groups: TRG4-5-TRG1-2
logFC logCPM PValue FDR
PPBP -4.3340878 9.503884 3.564802e-11 9.125894e-08
CDK6 -1.5518198 8.712466 1.458599e-07 1.867006e-04
IL1B 1.7324695 9.178351 2.623373e-05 1.908504e-02
CXCL8 1.6455933 8.340310 3.129262e-05 1.908504e-02
EGR1 0.8468036 8.652308 4.432857e-05 1.908504e-02
IFIT2 0.8957873 7.535228 5.199642e-05 1.908504e-02
IL6 1.3926323 6.951407 5.218565e-05 1.908504e-02
BDNF 1.4176689 6.605966 7.471018e-05 2.134076e-02
PTGS2 1.4746062 8.352272 7.547266e-05 2.134076e-02
FOS 0.9891503 9.263358 8.336234e-05 2.134076e-02
```

I have edited your post to format your code correctly. Bioconductor is now using markdown for posts, which means that you have to insert four spaces before each line of code in order for it to be recognised as code.

37kYou need to show the code you used for your edgeR and DESeq2 analyses. Otherwise we have no way to tell whether either of your analyses are correct.

37kThank you I will add my code to the post, I just know the sign of top genes in two method is completely flipped :(

10