Question: A puzzle about the results of differential genes
0
gravatar for llkxiaolan
2.2 years ago by
llkxiaolan0
llkxiaolan0 wrote:

I use the limma package to analyze the data, extract the genetic differences, but in the list of results, adj.p.value are basically the same, which is why, with the same code, analysis of other data, it did not encounter this problem, it is the problem of data. 

Here are the results of  data analyzed using the code :

  logFC AveExpr t P.Value adj.P.Val B
1449938_at 0.913685 9.095604 7.035732 0.000213 0.999936 -2.24783
1424967_x_at 1.136483 5.485582 6.265933 0.000432 0.999936 -2.37058
1460719_a_at 1.267538 8.413155 5.994509 0.000563 0.999936 -2.42196
1449937_at 0.958864 8.878113 5.92327 0.000605 0.999936 -2.43625
1418726_a_at 0.890958 4.738728 5.710449 0.00075 0.999936 -2.4811
1427004_at 0.90456 5.830647 5.64532 0.000802 0.999936 -2.4955
1419758_at 1.167344 7.691656 5.599396 0.000841 0.999936 -2.50585
1418086_at 0.988556 6.526427 5.59649 0.000844 0.999936 -2.50651
1422411_s_at 0.96971 7.66573 5.377632 0.001063 0.999936 -2.55825

 Here is the code I use:

 library(affy)
AffyRawData<-ReadAffy(widget=TRUE)
data.class(AffyRawData)
par(mfrow=c(2,3))
image(AffyRawData[,c(1,2,3,4,5,6)])
library(simpleaffy)
Data.qc<-qc(AffyRawData)
plot(Data.qc)
library(RColorBrewer)
library(affyPLM)
Pset<-fitPLM(AffyRawData)
colors<-brewer.pal(12,"Set3")
Mbox(Pset,ylim=c(-1,1),col=colors,main="RLE",las=3)
boxplot(Pset,ylim=c(0.95,1.22),col=colors,main="NUSE",las=3)
data.deg<-AffyRNAdeg(AffyRawData)
plotAffyRNAdeg(data.deg,col=colors)
legend("topleft",rownames(pData(AffyRawData)),col=colors,lwd=1,inset=0.05,cex=0.5)
AffyRawDatarma<-rma(AffyRawData)
boxplot(AffyRawDatarma,col=colors,las=3,main="RMA")
library(limma)
eset<-exprs(AffyRawDatarma)
design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2)))
colnames(design) <- c("group1", "group2")
contrast.matrix <- makeContrasts(contrasts="group2-group1",levels=design)
design
fit <- lmFit(eset, design)
fit1<- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit1)
dif<-topTable(fit2,coef="group2-group1",n=nrow(fit2),lfc=log2(1.5))
dif<-dif[dif[,"P.Value"]<0.05,]
head(dif)

Is there anyone who can help me explain this problem? Thank you very much 

                 

 

limma • 495 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by llkxiaolan0
Answer: A puzzle about the results of differential genes
0
gravatar for Gordon Smyth
2.2 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

This isn't a problem -- it just means there are no significantly differentially expressed genes.

ADD COMMENTlink written 2.2 years ago by Gordon Smyth39k

Sorry, I don't understand. You mean the difference is very small, right? I can't use adj.p.value as a filter condition. Should I use P.Valve? Thanks very much 

ADD REPLYlink written 2.2 years ago by llkxiaolan0
Answer: A puzzle about the results of differential genes
0
gravatar for llkxiaolan
2.2 years ago by
llkxiaolan0
llkxiaolan0 wrote:

Sorry, I don't understand. You mean the difference is very small, right? I can't use adj.p.value as a filter condition. Should I use P.Valve? Thanks very much 

ADD COMMENTlink written 2.2 years ago by llkxiaolan0
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