Metabric version problem

[jeitziner]

Hi team,

We have taken METABRIC data 6 months ago and had 2509 patients when accessing the data through cbioportal (clinical is fine) but the MRNA slot now only has 1980 patients. Probably this was also the case 6 months ago, but when I generate the same figures I did then I get different results (take one gene do median separation and survival, not the same results). Did the number of patients change or the expression? Do you have an idea why and can you provide us back with the older version ?

I am tagging here @rmadupuri as I see this is the person who did an update 6 months ago!

Thanks a lot and best wishes,

Rachel

[rmadupuri]

Hi @jeitziner, thanks for reaching out!

There have been no changes to the expression data in the METABRIC study for the last six months, except for updating a few outdated gene symbols to newer ones. Although we corrected the expression sample count from 1904 to 1980 in November of last year, it has remained 1980 since then. I don't see any data changes recently. If you have saved the results from six months ago, sharing them would be helpful for us to examine closely.

[jeitziner]

Hi @rmadupuri ,

This is exactly it we manage to find as well that we actually had 1904 patients. Can you provide us with the IDs of the 1904 patients such that we could go back to the previous version ?

Thanks a lot !

Best wishes!

[rmadupuri]

Hi @jeitziner, the files at https://github.com/cBioPortal/datahub/tree/4236c845980fe8bbf0492c71f11c07e88c6f65a0/public/brca_metabric shows the data before the expression update last year. Please note that, the latest version includes a reannotation of the Illumina probes, resulting in changes to data values shared by the author. To derive the same results, you will have to analyze the older version independently.

[jeitziner]

Hi @rmadupuri

Thanks so much for the explanations we were able to reproduce old results, just curious to see everything change so much. Also the 80 samples that have been added were they recently sequenced or, if I understood correctly from the link you sent they were actually just missing before on the cbioportal ?

Again thank you so much now everything is much clearer.

Best wishes,
Rachel