Contents

1 B cell dataset

Human B-cell expression dataset The human B-cell dataset (Gene Expression Omnibus series GSE2350) consists of 211 normal and tumor human B-cell phenotypes whose expression was profiled on Affymatrix HG-U95Av2 arrays, and it is contained in an ExpressionSet object with 6,249 features x 211 samples.

library(bcellViper)
data(bcellViper)
dset
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 6249 features, 211 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: GSM44075 GSM44078 ... GSM44302 (211 total)
##   varLabels: sampleID description detailed_description
##   varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation:
dataset <- exprs(dset)

2 PCAGenomicSignature

Constructed from 1,399 human RNAseq datasets.

wd <- "~/data2/PCAGenomicSignatureLibrary/refinebioRseq/canonicalPathways_v2"
fname <- "refinebioRseq_canonicalPathways_PCAmodel_hclust.rds"
PCAmodel <- readRDS(file.path(wd, fname))
PCAmodel
## class: PCAGenomicSignatures 
## dim: 7951 12436 
## metadata(7): cluster size ... MeSH_freq updateNote
## assays(1): model
## rownames(7951): 5S_rRNA 7SK ... SLC16A3 SLC38A2
## rowData names(0):
## colnames(12436): PCcluster1 PCcluster2 ... PCcluster12435
##   PCcluster12436
## colData names(3): PCcluster studies silhouetteWidth
## trainingData(2): PCAsummary MeSH
## trainingData names(1399): DRP000499 ERP023890 ... SRP188526 SRP189762

3 Interactive validation output

val_all <- validate(dataset, PCAmodel) 
plotValidate(val_all, interactive = TRUE)