Microarray data normalization
1
0
Entering edit mode
23 months ago
seta ★ 1.7k

Dear all,

Sorry for such a basic question, but I got confused. As far as I know, the RMA method implemented in affy package is a standard method for microarray data normalization. Could you let me know if the main code data.rma.norm = rma(raw.data) normalize data in three stages, background correction, quantile normalization, and log2 transformation? So the output of the above code is log2 expression value, yes? or there is another story?

Many thanks

RMA microarray normalization • 1.0k views
ADD COMMENT
0
Entering edit mode
23 months ago

Yes, on default settings, it will perform:

  1. background correction
  2. quantile normalisation
  3. log [base 2] transformation

By the way, you may want to switch over to oligo::rma(), which is more 'transportable'.

Kevin

ADD COMMENT
0
Entering edit mode

I want to perform RMA normalization on a data frame, how should I proceed? Should I perform each step individually using the limma package??

Parin Vyas

ADD REPLY
0
Entering edit mode

What is the source of the data contained in the data frame? Please describe it a bit more

ADD REPLY
0
Entering edit mode

Datafame contains raw intensities of proteomics data, I would like to preprocess it for DE analysis.

ADD REPLY
0
Entering edit mode

Please consult the company who produced the data. It may require a different type of processing than what you think.

ADD REPLY
0
Entering edit mode

ok thank you

Parin vyas

ADD REPLY

Login before adding your answer.

Traffic: 1452 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