Question: differential expression analysis from microarray data
0
gravatar for au.rinki.bio
7 months ago by
au.rinki.bio10
au.rinki.bio10 wrote:

hello, I am working microarray data analysis using limma package. my data consist 4 normal sample and 8 cancerous sample using the following command line l

ibrary(affyio)
library(affy)
ovarian<-make.cdf.env("HGU133A_Hs_ENSG.cdf")
data<-ReadAffy(cdfname='ovarian')
data
data<-ReadAffy()
eset <- rma(data)
exprSet <- exprs(eset)
ph<-pData(eset)
ph
head(pData(eset))
p_disease<- c("control","control","control","control","case","case","case","case","case","case","case","case")
p_disease
design <- model.matrix(~factor(p_disease))
d<-colnames(design) <- c("case","control")
d
contrast.matrix <- makeContrasts(case-control, levels=design)
design
fit <- lmFit(eset, design)
r<-eBayes(fit)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit3 <- eBayes(fit2)
options(digits=2)
genes
getwd()
gene<- topTable(fit3, coef=1, adjust="BH",lfc=2, p.value=0.05)
write.table(gene,"d1.xls",sep="\t",col.names = NA)

the problem is that i get differentially expressed genes with positive value how is it possible.

limma microarray • 419 views
ADD COMMENTlink written 7 months ago by au.rinki.bio10

Do you mean you only get positive values?

ADD REPLYlink written 7 months ago by igor7.1k

i got fold change with only positive value. I want to filterer differentially expressed genes with log fc>±2 .

ADD REPLYlink written 7 months ago by au.rinki.bio10

Have you tried running topTable() without lfc parameter? This way you can see the distribution of your fold changes. Maybe none of the negative fold changes are more than 2.

ADD REPLYlink written 7 months ago by igor7.1k

positive value of what?

ADD REPLYlink written 7 months ago by WouterDeCoster35k

sorry for miscommunication, actually I want to filter differentially expressed gene with log fc> ±2. but I got genes with only positive value. I hope it is clear to you.

ADD REPLYlink written 7 months ago by au.rinki.bio10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1275 users visited in the last hour