Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes.

ABSTRACT:

Motivation

Medulloblastoma (MB) is a brain cancer predominantly arising in children. Roughly 70% of patients are cured today, but survivors often suffer from severe sequelae. MB has been extensively studied by molecular profiling, but often in small and scattered cohorts. To improve cure rates and reduce treatment side effects, accurate integration of such data to increase analytical power will be important, if not essential.

Results

We have integrated 23 transcription datasets, spanning 1350 MB and 291 normal brain samples. To remove batch effects, we combined the Removal of Unwanted Variation (RUV) method with a novel pipeline for determining empirical negative control genes and a panel of metrics to evaluate normalization performance. The documented approach enabled the r

SUBMITTER: Weishaupt H 

PROVIDER: S-EPMC6748729 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature