Question: differential expression analysis from microarray data
0
gravatar for au.rinki.bio
2.3 years ago by
au.rinki.bio10
University of Allahabad, India
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 • 1.4k views
ADD COMMENTlink written 2.3 years ago by au.rinki.bio10

Do you mean you only get positive values?

ADD REPLYlink written 2.3 years ago by igor11k

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

ADD REPLYlink written 2.3 years 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 2.3 years ago by igor11k

positive value of what?

ADD REPLYlink written 2.3 years ago by WouterDeCoster44k

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 2.3 years ago by au.rinki.bio10
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