In the RNAseq data table, possible values for tumorType are:
'Cutaneous Neurofibroma',
'High Grade Glioma',
'Low Grade Glioma',
'Malignant Peripheral Nerve Sheath Tumor',
'Meningioma',
'Neurofibroma',
'None',
'Plexiform Neurofibroma',
'Schwannoma'
What does "None" mean here?
Was the sample NOT taken from a tumor? From normal tissue? Normal Schwann cells from an NF1/NF2 patient, maybe?
Or does it simply mean that information about the tumor type is not available?
Thanks for clarifying this!
Created by Andreas Kraemer akraemr Yep, this was done overnight. I had to run some of the updates manually this morning before jumping on the plane, but it should be there. Let me know if you discover any issues I see modelOf now
```
array(['Cutaneous Neurofibroma', 'Neurofibroma',
'Malignant Peripheral Nerve Sheath Tumor',
'Plexiform Neurofibroma', 'normal', 'Low Grade Glioma',
'High Grade Glioma', 'Meningioma', 'schwannoma', 'NF1 tumor',
'Malignant peripheral nerve sheath tumor', 'Schwannoma',
'Ependymoma', 'Ganglioglioma', 'Other'], dtype=object)
```
As an aside - super-clean metadata for these samples can be confusing, especially when more specific tumor types are occasionally being defined, clinical metadata is incomplete or inconclusive, and we have cell line models that are meant to imitate biology but aren't bona fide tumors, for example. Just worth considering when you work with the data! Hi there,
"None" means that it is not from a *bona fide* tumor cell.
For example for tumorType:
A normal schwann cell line would be None
A genetically engineered NF1 -/- schwann cell line would also be None
An NF1 -/- plexiform neurofibroma cell line would be Plexiform Neurofibroma
I'll be adding another metadata column, modelOf, that will hopefully help clarify this. In the above example, modelOf would be:
A normal schwann cell line would be Normal
A genetically engineered NF1 -/- schwann cell line would be "NF1 tumor" (we can't be more specific based on the information we've been given)
An NF1 -/- plexiform neurofibroma cell line would be Plexiform Neurofibroma
I hope to add this column later today. Stay tuned!