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Clarification on microarray equation

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

r genome
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updated by theobroma22 theobroma22 • written by asifnax • asifnax

Anyone has an answer for this ?

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written by asifnax • asifnax

1 answer

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."

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written by theobroma22 theobroma22

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