Is it possible to apply limma on metabric data?
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Entering edit mode
9 months ago
dare_devil ★ 1.5k

I have downloaded the microarray expression data afrom metabric and followed below mentioned steps. Is it the right way to perform the DEG analysis?

library(limma)
library(marray)
list.files()
#Read the expression data
mRNA  = read.delim("ER+VE_Post.txt",
                         sep='\t', row.names = 1, header = TRUE) #This is normalized expression data

#read the target file
targets = read.delim(file="targets.txt", header=T)
str(targets)

#Design model matrix
conditions<- targets$Group
head(conditions)
conditions = factor(conditions, levels=unique(conditions))
design = model.matrix(~0+ conditions)
colnames(design) = levels(conditions)
#Fit the model matrix
fit = lmFit(mRNA, design)
cont.matrix = makeContrasts(HvL=High-Low,
                            HvM=High-Moderate,
                            MvL=Moderate-Low,
                            levels=design)
fit2 = contrasts.fit(fit, cont.matrix)
fit2 = eBayes(fit2)

#Results
results<-decideTests(fit2,adjust.method="fdr",p=0.05)
summary(results)

#Save to local
write.fit(fit2,
          file="limma_er_pos_post.txt",
          adjust="fdr",
          results=results)
limma metabric mRNA DEG • 290 views
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