author: Pablo Riesgo (priesgo@uoc.edu) date: 08/11/2015
library("RTCGAToolbox")
firehose_datasets = getFirehoseDatasets()
firehose_dates= getFirehoseRunningDates()
BRCA.dataset = getFirehoseData (dataset="BRCA", runDate=firehose_dates[1], RNAseq2_Gene_Norm = TRUE, RPPA=TRUE)
OV.dataset = getFirehoseData (dataset="OV", runDate=firehose_dates[1], RNAseq2_Gene_Norm = TRUE, RPPA=TRUE)
407 BRCA + 201 ovary cancer samples
12880 gene expression + 55 protein expression variables are far too many to plot...
Joint analysis
Joint analysis
The 2 first PCs explain 34.05% and 11.55% of the variance
Labeled items are the top 100 variables
Samples
Variables
Heatmap
Network
Matches between MCIA and sPLS top 100 and known oncogenes and tumor supressor genes
Matches between MCIA and sPLS enriched pathways in Reactome
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