I want to do a list for differencialy expressed genes with txt data from this experiment: GSE38376
I downloaded the txt file read it in R and normalized it:
> idata <- read.ilmn("GSE38376_non-normalized.txt",probeid = "PROBE_ID",expr="SKBR")
> data_nobg <- backgroundCorrect(idata,method="normexp")
> data_norm <- normalizeBetweenArrays(data_nobg,method="quantile")
data_ norm is in Elist class
Now i would like to select the differentially expressed genes with creating a model.matrix and then do the lmFit but do i have to do the step ExpressionSetillumina? if i do how do i do do it , with the class Elist? If id ont how do i continue??