How to get a list of differentialy expressed genes with data from Illumina array?
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6.3 years ago
kanacska ▴ 10

Hi,

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??

 

Thanks, 

Anna

microarray R limma illumina • 1.5k views
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