[R] (no subject)

[Rasmus Liland]

On 2020-12-11 22:09 +0500, Anas Jamshed wrote:
> 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

Sorry, I think I am too tired atm.  I 
took this pneumonia vaccine, and it 
really banged me up you know ...

Maybe someone else can row this ship 
ashore again ...

R