limma DEG analysis with count matrix as input

Question

[asumani]

Hi,

I am trying to make a meta-anlaysis between microarray and RNA datasets. My aim is to generate normalized count matrix for each set. I try to use raw data when available and process them myself. However, I have to start from GEO Series Matrix for microarray data.

Microarray data pre-processed already as:

"The raw microarray data were processed by Lumi package in R, with background adjustment, variance-stabilizing transformation, and quantile normalization within each batch."

I believe this is a florescent signal normalization. I want to have the next step of normalization for DEG analysis with limma package. Yet, at that point I am confused where to start, which object to create etc. I need to process count matrix, not .CEL files.

Thanks in advance

[ATpoint]

Microarrays do not have counts, but fluorescence intensities. Please read the limma manual, it contains all necessary code for a standard analysis. CEL files are the raw data of microarrays of the manufacturer Agilent. Have a look at the oligo package to read and normalize CEL via the rma algoritm.

[asumani]

I have processed data, not CEL data. I was unsure about how to process further, So, I prepared a design matrix and used intensity(columns as sample, rows as probes data as input.