Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

James P.R. Hacking, Dean Thompson, Edward C. Schwalbe, Steven C. Clifford, Daniel Williamson*

*Corresponding author for this work

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Abstract

Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier.

Original languageEnglish
Article number102509
JournalSTAR Protocols
Volume4
Issue number3
Early online date18 Aug 2023
DOIs
Publication statusPublished - 15 Sept 2023

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