Metabric Microarray Expression Data

[gokc...@gmail.com]

Hi All,

I would like to know the details about  Metabric mRNA Expression z-Scores (U133 microarray only).

So the data obtained using Affmetrix GeneChip™ Human Genome U133 Plus 2.0 Array. However, how does it normalized. What does it mean by Z-scores? How does it z-scored ? Are the values log10 ?

I would be really glad if you could give me more details.

Best Regards,

Gokce

[Ritika Kundra]

Hi Gokce,

 

Apologies for the delayed response.

 

The platform used by the Metabric project is actually the Illumina Humanv3 platform, which is log2 intensities, very similar to Affymetrix data. We will fix this description error soon.

 

The portal then dynamically calculates the Z-Scores for each gene and sample. This description of how Z-SCORES are calculated is from our FAQs:

 

For mRNA and microRNA expression data, we typically compute the relative expression of an individual gene and tumor to the gene's expression distribution in a reference population. That reference population is all samples that are diploid for the gene in question (by default for mRNA), or normal samples (when specified), or all profiled samples. The returned value indicates the number of standard deviations away from the mean of expression in the reference population (Z-score). This measure is useful to determine whether a gene is up- or down-regulated relative to the normal samples or all other tumor samples.

 

You can use the gene scores when running a query, and you can display z-scores and actual levels on the Plots tab.

 

Thanks,

Ritika

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