How to find upregulated and downregulated genes for my microarray data with limma

Question

[kai_bio]

I have annotated the .cel files and got the log2 transformation values of 12 gastric effected patients and 15 normal (control) samples patients data and 54675 probes. I want to find DEGs from the log2 transformation values with limma package.

library(affy)
library(affyQCReport)
library(limma)
library(tkWidgets)
library(oligo)

list.celfiles()

names=list.celfiles()
names=dir(pattern = "CEL.gz")

#reading celfiles from oligo package
array = read.celfiles(names)

#converts an AffyBatch object into an ExpressionSet object using the robust multi-array average (RMA) expression measure.
eset = rma(array)


# Finally, save the data to an output file to be used by other programs, etc (Data will be log2 transformed and normalized)
write.exprs(eset, file="array.txt")

#Read CEL files into an Affybatch.
array = ReadAffy(widget=TRUE)

library(affyQCReport)
affyQAReport(array)
arrayaffy = read.table("array.txt", header = TRUE, sep="", row.names=1)

library(limma)
targets <- readTargets("array.txt")
targets

How do I approach from then on? Thank you in advance

[Kevin Blighe]

It is likely not necessary to load both affy and oligo packages here, or, are you only using affy so that you can generate the QC report via affyQAReport()? Which array type are these samples? - probably Affymetrix U133, right?

Also, read.celfiles(names) will not return an AffyBatch object, as indicated in your comment in your code - it returns an ExpressionSet.

Your next step will be to specify a design formula and create a contrasts matrix. Can you first let us know what is in your targets file and which conditions / groups you want to compare?

[Mark]

Can you please properly format your code? Use the button that has 101010 on it.

[Kevin Blighe]

I have formatted it this time around. koushik.vf09, please use the 101 010 button in future, if possible.

[kai_bio]

I apologize for the wrong format of the code and Thank you very much for formatting the code, will make sure that wont happen again.