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Normalized data were produced by Normalize to 75 percentile sift protocol and baseline to median of control sample protocol''. Arrays were filtered on expression (20-100)th percentile in raw data.''","name":"normalization data transformation","parameters":[{"@id":"#139850538236608","parameterName":{"@id":"SXVltIvFoX3BIgVxN4vLgKxRdQgAYr5Bqf7YulLu","annotationValue":"Normalized Data File Name","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"grpPRfpK2IY0qyMGtTQ24NTipWEi9w8qaf3FS1xK","annotationValue":"normalization data transformation","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139850538235888","comments":[],"components":[],"description":"Data were processed as described in GL-DPPD-7112 (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Agilent_1-channel/Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Agilent_1-channel/Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md</a>), using NF_MAAgilent1ch version 1.0.3 (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.3/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_1.0.3/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch</a>). In short, a RunSheet containing raw data file location and processing metadata from the study's *ISA.zip file was generated using dp_tools (version 1.3.1). The raw array data files were loaded into R (version 4.1.3) using limma (version 3.50.3). Raw data quality assurance density, pseudo image, MA, and foreground-background plots were generated using limma (version 3.50.3), and boxplots were generated using ggplot2 (version 3.4.0). The raw intensity data was background corrected and normalized across arrays via the limma (version 3.50.3) quantile method. Normalized data quality assurance density, pseudo image, and MA plots were generated using limma (version 3.50.3), and boxplots were generated using ggplot2 (version 3.4.0). Ensembl gene ID mappings were retrieved for each probe using the Ensembl database ftp server (ensembl.org, release 107). 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