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Expression data for all three platforms were obtained as described in [ 9].
Data from Agilent platforms were obtained from Agilent Feature Extraction software and pre-processed in GeneSpring GX 11 (Agilent Technologies, Santa Clara CA) using median-background subtraction on a per-study basis.
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mRNA expression data from next generation sequencing platforms is obtained in the form of counts per gene or exon.
Genotypes for only these 27 SNPs were obtained from the Center for Applied Genomics, and no additional genotypes on this platform were obtained or analyzed.
A total of 569 DNA copy-number profiles (Affymetrix GenomeWide SNP 6.0 platform) were obtained.
To obtain sufficient statistical confidence in the data analysis, for each biological replicate (MRP1 and MRP2), five technical replicates on each platform were obtained, with an exception on Illumina.
Genotyping data on each platform were obtained from the VCF files and PLINK/PED files using a set of in-house scripts; then, the genotype concordance and accuracy were calculated.
GE profiles of the same ALL specimens, measured with the Affymetrix HG-U133A platform, were obtained from GEO (GSE12995; [ 45]) and preprocessed with the RPA algorithm [ 46] and EntrezID-based custom chip definition file (v13; [ 47]).
The inverse solutions and parasitic rotations of the moving platform are obtained and analyzed, which are based on a parallel mechanism with real parameters.
For the former, the mean value and the standard deviation of the weight of a gravity-based platform are obtained to satisfy two reliability constraints related to overturning and sliding on the seabed.
Mixing these two aspects as well as envisaging direct use of the top-down elements into the bottom-up approach, the UML use case diagram of the required functionalities of the eGRASP platform was obtained (Fig. 2).
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