Microarray data normalization

Question

[seta]

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

Answer 1

[Kevin Blighe]

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

[parinv]

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

[Kevin Blighe]

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

[parinv]

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

[Kevin Blighe]

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

[parinv]

ok thank you

Parin vyas