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SNPs with an imputation score > 0.8 and present originally in one or both datasets were extracted and 417,708 SNPs remained for all further analyses.
The methylation signals of the 25,978 shared CpG sites by 27 K and 450 K datasets were extracted and the methylation status of each probe was defined according to the beta-value.
For each pairwise comparison between two datasets, genes for which non-zero values existed in both datasets were extracted, and for each gene the fold difference in reported values was calculated.
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The nature of the atomic planes in both datasets was extracted and analysed.
In the contamination screening step, 18S rRNA reads of each dataset were extracted and mapped to SILVA 18S database [6].
The TUTR dataset was extracted and constructed by the authors while the EID is a large subset of an existing database [ 11, 12].
These lower values are expected partly because the test datasets were extracted from Swiss-Prot, and partly because TrEMBL is a much larger database.
First, the target genes of DE-miRNAs found by at least 3 datasets were extracted, then mapped to function and pathway databases, e.g. GO [ 16], KEGG [ 17, 18] and GeneGO (GeneGo, Inc), to identify PCa-associated functions and pathways.
As regards the evaluation of predictive performance and stability of selected gene subsets, the parameters of our methodology were set as follows: a number P = 20 of reduced datasets were extracted from the original dataset, and each reduced dataset contains a fraction f = 0.9 of the original samples.
A compendium of gene-expression datasets were extracted from AtGenExpress, including 459 biosamples and 1,027 slides on Affymetrix platform (ATH1) (based on Feb. 20th, 2007) for the whole Arabidopsis genomes.
Analytic datasets were extracted, underwent a final quality-control analysis and were converted to SAS® (SAS Institute, Cary, NC) and SPSS® 12.0 (SPSS , Inc Chicago, IL) datasets.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com