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The processing and statistical analysis of the data was performed by using the Statgraphics Plus 5.0 software package (Manugistics, Inc. Rockville, MD).
Further processing and statistical analysis of data was done using the R/Bioconductor software suite (Gentleman et al., 2004).
DESeq [ 20] and R [ 21] were used for the post processing and statistical analysis of these read counts.
Quality control (QC) assessment, data processing, and statistical analysis of array data were conducted in R [ 124] using packages from the Bioconductor project [ 125].
Processing and statistical analysis of gene expression data was performed using Expressionist Pro v4.5 (Genedata, Basel, Switzerland), if not indicated differently.
The download, processing and statistical analysis of the data collected during the study will be performed using PASW Statistics 18 software (SPSS).
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AK performed pre-processing and statistical analysis of the microarray data.
Pre-processing and statistical analysis of the fMRI data were carried out using SPM5 software (www.fil.ion.ucl.ac.uk/spm/).ac.uk/spm/
All pre-processing and statistical analysis of microarray data was performed in R [ 50] version 2.4.1 using Bioconductor packages release 1.9 [ 51].
AgiMicroRna is a rational collection of Bioconductor functions that have been wrapped into specific functions in order to ease and systematize the pre-processing and statistical analysis of Agilent microRNA data.
Subsequently, signal intensities were VST-transformed (variance-stabilizing transformation) and RSN-normalized (robust spline normalization) using the Lumi package in R. Post-processing and statistical analysis of microarray data was carried out in Matlab.
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