mRNA Expression: z-score to diploid or all samples

[M B]

Hi Heros,

Does anyone know the difference between:

"mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM)"

and

"mRNA expression z-scores relative to all samples (log RNA Seq V2 RSEM)"?

I've read the description in FAQ, some online comments, plus previous communication, but I still did not get it.

Also the previous communication suggests, that they both lead to almost the same results. When I tried both of them to explore survival curves in Breast Invasive Carcinoma (TCGA, Firehose Legacy), I got completely different curves (results).

Any clue?

[Matthijs Pon]

Hi,

This is the link to the explanations for the Z-Score calculations. I've summarised below them to hopefully make it more clear:

- Diploid Z-Scores are calculated using diploid samples only. Meaning that the expression values are normalised to the expression distribution of unaltered copies of the gene.
- All samples Z-Scores, on the other hand, are calculated using all samples, meaning that altered copies also affect the normalisation process.

How are you investigating the survival curves? The KM Plot: Overall Survival (months) does not seem to change in the Breast Invasive Carcinoma (TCGA, Firehose Legacy) study when selecting one of the subsets. Can you provide a link or screenshot?

I hope this explanation helps! Please hit reply all when responding, so our continued conversation is captured by the cBioPortal google group.

Kind regards,

Matthijs Pon

Data Engineer cBioPortal

E matt...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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