curatedPCaDatasets_barwick: Barwick et al. MAE-object
In Syksy/curatedPCaData: Curated Prostate Cancer Data

curatedPCaDatasets_barwick

R Documentation

Barwick et al. MAE-object

Description

MultiAssayExperiment object containing gene expression (gex) and immune cell estimates for Barwick et al.

Format

A MAE object spanning 146 prostate cancer samples.

gex.logq: matrix with 482 rows and 146 columns, for the log-quantile normalized gene expression data
cibersort: matrix with 22 rows and 139 columns, of cibersort based deconvolution data
quantiseq: matrix with 11 rows and 139 columns, of quantiseq based deconvolution data
estimate: data.frame with 4 rows and 139 columns, of cell types based on ESTIMATE method
scores: matrix with 3 rows and 139 columns, of risk scores and AR scores
mcp: matrix with 4 rows and 139 columns, of mcp-counter based deconvolution data

Details

Barwick et al. uses an older customized DASL array; therefore its gene coverage is lower, and many downstream methods fail due to lack of gene overlap.