msisensor-pro
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Matched vs tumor_only scores
I have compared MSI scores for the same tumor samples between:
- its matched normal (
msi
) - a baseline of normals (
pro
)
I had 65 tumor and 58 normal samples of which 55 are matched.
In case 1 above, I used 55 matched samples and run the analysis for each normal-tumor pair.
In case 2, I used all 58 normal samples to create a baseline and compared each of tumor samples to this baseline.
I used default values for all parameters.
Between the two analysis, I got very different results for the same tumor samples in terms of somatic sites / MSI scores.
Case 1 gave none to very few events, resulting in around 0% MSI. Case 2 gave a range more than 1%, with a few samples up to 5-10% MSI.
How to explain this discrepancy? Which one to trust more?