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Table 2 Best combination of methods for each step: Summary of the best combination of algorithms for each view used to obtain the best grouping of patients that identifies significant sub-classes

From: MVDA: a multi-view genomic data integration methodology

  

(a)

(b)

(c)

(d)

Dataset

Views

Feature

Feature

Patients

Late

  

clustering

selection

clustering

integration

TCGA.BRCA

RNASeq

Pam

CAT-score

Kmeans

MF

 

miRNASeq

Pam

CAT-score

Pam

 

TCGA.OV

Gene Expression

Pam

Random Forest

DM

MF

 

Protein Expression

Pam

-

DM

 
 

miRNA Expression

Pam

-

DM

 

TCGA.GBM

Gene Expressions

Spectral

CAT-score

Kmeans

MF

 

miRNA Expression

Ward

-

Kmeans

 

OXF.BRCA.1

Gene Expressions

Pam

Random Forest

Ward

GLI

 

miRNA Expression

Pam

Random Forest

Kmeans

 

OXF.BRCA.2

Gene Expressions

Pvcluster

CAT-score

Kmeans

MF

 

miRNA Expressions

Pam

Random Forest

Kmeans

 

MSKCC

Gene Expressions

Pam

CAT-score

Kmeans

MF

 

miRNA Expressions

Pam

-

Pam

 
 

CNV

Spectral

CAT-score

Kmeans

 
 

Clinical

-

-

Pam

 
  1. In the feature selection column the symbol (-) means that feature selection was not executed because the number of features was small. Symbol (DM) in Patient clustering column means that same classification error was obtained with all the algorithms used
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BMC Bioinformatics

ISSN: 1471-2105

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