**0**wrote:

Hello guys,

One question I have met recently is that when i handle the GEO data(GSE100186) with limma package, the result by t~test I could get was about 1,561 different express genes. However ,when I chose paired t~test, I could get none genes when I set p.value= 0.05. I did not know what wrong with this or how could I deal with this case. The process I operated is as follows: t~test:

```
group_list<- c(rep("normal",4), rep("Tumor",4))
group_list<- factor(group_list, levels = c("Tumor","normal"))
group_list<- factor(group_list, levels = c("Tumor","normal"), ordered = F)
library("limma")
design<- model.matrix(~0+group_list)
colnames(design)<- levels(group_list)
contrast.matrix<- makeContrasts(Tumor-normal, levels = design)
fit<-lmFit(exprSet, design)
fit2<- contrasts.fit(fit, contrast.matrix)
fit2<- eBayes(fit2)
allDiff<- topTable(fit2, adjust="fdr", coef = 1, number = Inf)
```

paired~T test:

```
pairinfo = factor(rep(1:4,2))
group_list<- c(rep("tumor",4), rep("normal",4))
group_list<- factor(group_list,levels = c("tumor","normal"),ordered = F)
design=model.matrix(~ pairinfo+group_list)
fit=lmFit(exprSet,design)
fit=eBayes(fit)
allDiff_pair=topTable(fit,adjust='BH',coef=2,number=Inf,p.value=0.05)
```

**69k**• written 16 months ago by xaimi0813 •

**0**

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