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BeadChip data files are analyzed with Illumina's GenomeStudio gene expression module and R-based Bioconductor package to determine gene expression signal levels [47].
Reference sequence file is not required when BAM/SAM files are analyzed.
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Gels have been exposed with the ChemiDoc analyzer and the output files were analyzed with Image J to obtain the density profiles of the bands.
Results Twenty-nine files were analyzed.
The PKL files were analyzed using the MASCOT search engine.
Then the csv files were analyzed in a MATLAB platform.
Image files were analyzed using Hermes Dynamic Study display software V4.0 (Hermes Gold V2.10, Hermes Medical Solutions, Stockholm/London).
Data files were analyzed using FACSDiva™ software (BD).
The MGF files were analyzed using Proteome Discoverer 1.2 (Thermo Fisher Scientific).
Image files were analyzed using ImageJ software (NIH).
The output files were analyzed with MEGAN version 3.7.2 [32].
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