queries regarding data sets

[Summer Henderson]

Hi there,

 

We are using data from a few meningioma sets on your site. We had a couple queries regarding the mRNA data:

 

1. Where it is stated ‘relative to diploid’, does this mean that it is compared to a matched normal meninges sample?

 

2. Where the mRNA level is given as N/A does this mean that there has been no mRNA detected or that no mRNA was tested for this sample?

 

I tried to find this out with the user guides, but I could not find the answers.

 

Thank you in advance,
Summer Henderson

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[Benjamin Gross]

Hi Summer,

When we say ‘relative to diploid’, we do not mean matched normal.  We mean expression level is compared to other tumor samples that have diploid copy number.  Regarding N/A values it’s hard to say.  It it could be that the sample wasn’t profiled, but for one reason or another, when the data was curated, the measurement wasn’t provided.  You may be able to find more information if you follow the literature associated with the study.

Best,

Benjamin

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[Summer Henderson]

Thanks Benjamin.

Can you confirm what you mean by ‘other tumor samples that have diploid copy number’?

Summer

[Benjamin Gross]

Hi Summer,

log-transformed z-scores are computed for each sample/gene against the average expression level of the tumor samples in the cohort that are diploid for the gene (no amplifications or deletions)

Best,

Benjamin