limma DEG analysis with count matrix as input
0
0
Entering edit mode
10 months ago
asumani ▴ 70

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

meta-analysis limma microarray • 535 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1259 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6