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The comparison is done using the implementation provided by the respective authors.
The PCA was performed using the implementation of the R package FactoMineR version 1.26 (Lê et al. 2008); the permutational MANOVA was carried out using the implementation provided by the R package vegan version 2.0-10 2.0-10en et al. 2013).
Hence, for the problems considered here it is outperformed by other methods like DHC, SOLNP, or FMINCON.> -wrap-foot> Optimization settings and results obtained for each of the benchmarks with the eSS method, using the implementation provided in the AMIGO toolbox.
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For SSIM, we used the implementation provided by [16].
To run the experiments we used the implementation provided with MIA [ 23].
For CF, we used the implementation provided by the R/CRAN package 'party' version 1.0-9 [ 45].
For all the above feature selection techniques we used the implementation provided by the WEKA machine learning environment [ 31].
For RF, we used the implementation provided by the R/CRAN package 'randomForest' version 4.6-7 [ 44], which follows the original algorithm proposed by Breiman 2001 [ 20].
These data were calculated using the C++ implementation provided by the authors as open-source software.
For the FFD method, the implementation provided by the ElastiX library [ 32] was used.
GeneChip data were analyzed by the robust multiarray analysis (RMA) procedure [ 37] using the implementation of RMA provided by the open source bioconductor project http://www.bioconductor.org[ 38].
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