What are RMA units?
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6.0 years ago
lotus28 ▴ 70

What exactly are RMA-units I get after normalizing affymetrix data?

These are relative expression log2 units. But relative to what? What is RMA = 0?

rma affymetrix array • 8.0k views
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6.0 years ago
natasha.sernova ★ 3.9k

See this link to a presentation:

http://www.ub.edu/stat/docencia/bioinformatica/microarrays/ADM/slides/2_PreprocessingMicroarrayData-2-Preprocessing%20and%20Normalization.pdf

And also this link to some discussion on the topic:

https://www.researchgate.net/post/What_exactly_is_the_unit_of_measure_in_microarray_experiments

" Michael B Black · ScitoVation The raw data is effectively unitless as it is simply relative signal intensity. Flourescence is measured by a photo multiplier tube or charge-coupled device and signal scaled across the range of detection for the platform. The starting data is thus simple relative signal values without units, based effectively on simple counted photons by the PMT or CCD. "

" Prafull Kumar Singh · University Medical Center Freiburg Micro array chip contain multiple probes for each gene. After completion of the experiment a .dat is generated which is a image showing the intensity of each probe in a digital format. Now it is converted into .cell file which contains the real probe intensity numerical values.The higher the probe intensity higher is the expression of the gene. But its meaningless until you compare it with the intensity of same probe in control sample. These probe intensity values are preprocessed (Background correction, normalization, Perfect match correction and Summarization) using diff algorithms (RMA, Mas5). The normalized probe intensity values are further used for calculation of relative gene expression i.e treatment vs control to get the fold change. The positive and negative values indicates up-regulated and down-regulated genes in treatment group when compared to control."

etc...

An initial experiment reference:

http://biostatistics.oxfordjournals.org/content/4/2/249.full.pdf

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