Clarification on microarray equation

Question

[asifnax]

Hi,

There is a old bioinformatic method called RMA but can be applied to exon arrays (FIRMA).

https://academic.oup.com/bioinformatics/article/24/15/1707/265243/FIRMA-a-method-for-detection-of-alternative

Can anyone explain how RMA and FIRMA are different ? - and why in equation (3) do they add the probe effect and chip effect together?

a breakdown to a non-bioinformatician would be great.

Thank you

[asifnax]

Anyone has an answer for this ?

Answer 1

[theobroma22]

I read the nice article you provided.

Simply, in the case of your exon array RMA is analyzing the transcript expression while FIRMA is analyzing the exon for alternative splicing. So, for equation 3 the cell chip is orientated such that the transcripts are grouped together, and the 'Ci' variable is accounting for "noise."