Hi! I conducted DGE analysis between 2 groups of cell lines MYCN amplified vs MYCN non amplified.

Cell lines in the MYCN non amplified group had these FPKM values for MYCN gene: 5.182582, 3.104376, 4.962478

Cell lines in the MYCN amplified group had these FPKM values for the MYCN gene: 101.2204, 301.8182 , 280.6712

Now visually there is a marked difference between these two groups and should be significantly different regardless of the transformation/normalization. However, upon applying logCPM, lmFit and eBayes, I get the following log FC/p.vals for MYCN

logFC: 1.27382121 p.value : 0.8228308 adj. P.value: 0.92421833

why is this change so insignificant??

I'm hoping to catch the eye of Gordon Smyth on this post!

Code shown below

```
logCPM_SD_rep <- cpm(samp.SD.representative+1, log=TRUE, prior.count=3)
fit.sd.rep <- lmFit(logCPM_SD_rep, design.sd.rep)
fit.sd.rep <- eBayes(fit.sd.rep, trend=TRUE)
topTable(fit.sd.rep, coef=ncol(design.sd.rep))
contr_SD<-makeContrasts(group.sd.repAmp - group.sd.repNot_Amp, levels = colnames(design.sd.rep))
tmp.sd.rep<-contrasts.fit(fit.sd.rep,contr_SD)
tmp.sd.rep <- eBayes(tmp.sd.rep)
top.table.sd.rep <- topTable(tmp.sd.rep, sort.by = "P", n = Inf)
head(top.table.sd.rep, 20)
```

Gordon Smyth