(no subject)

On Fri, Dec 11, 2020 at 9:51 PM Rasmus Liland wrote:

Say, how do I create fit3, eset, design,
etc. ...

R

library(oligo)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pd.hg.u133.plus.2")
list.celfiles()
setwd("C:/Users/USER/Desktop/RNA_Seq")
list.celfiles()
names = list.celfiles()
array = read.celfiles(names)
array
eset = rma(array)
write.exprs(eset, file = "data_normalized.txt") #this will be your
normalized data by rma
eset
targets<-read.delim(file="targets.txt", header=T)
targets<-read.delim(file="E-MTAB-5716.sdrf.txt", header=T)
targets

eset <- eset[[idx]]

design <- model.matrix(~0+ eset)
design
fit <- lmFit(eset, design)
fit

cont.matrix <- makeContrasts(eset, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2
fit3 <- eBayes(fit2, 0.01)
fit3
tT <- topTable(fit3, adjust="fdr", sort.by="B", number=1250)
tT