z-score RPPA protein and phosphoprotein

[Maria Rosaria De Filippo]

Dear cbioportal stuff,

I'm Maria Rosaria De Filippo a research fellow in MSKCC.

I downloaded normalized RPPA data (level3) from tcga Breast Cancer (nature 2012).

After that I calculated Z-score for one of the sample (TCGA-B6-A0RO) with PIK3CA mutations.

In cbioportal I selected Breast Cancer and Genomic Profiles: mutations, than I selected the sample of interest (for example TCGA-B6-A0RO), and finally gene of interest (for example PIK3CA) 

When I look at protein and phosphoprotein in cbioportal the z-score value is different.

How do you perform z-score calculation for protein and phosphoprotein ?

Best Regards,

Maria

[JianJiong Gao]

Hi Maria,

We calculate the RPPA zscore for a protein/phorphoprotein as follows:

1. calculate mean and standard deviation of the RPPA values of the
protein/phosphoprotein in the cohort.
2. calculate zscore for each sample, ie. (x-mean)/std, x being the
rppa value of the sample.

There could be some difference in the calculated values. As long as
the orders remain the same, I wouldn't worry too much. In the end, you
may have to set a threshold specific to each antibody and dataset
anyway. Zscore is just our way to have a default threshold.

Please feel free to contact us for more questions.

Best,
-JJ

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