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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 1.3.2). The raw array data files were loaded into R (version 4.1.3) using oligo (version 1.58.0). Raw data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0). The raw probe level intensity data was background corrected and normalized across arrays via the oligo (version 1.58.0) quantile method. Normalized probe level data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0). Normalized probe level data was summarized to the probeset level using the oligo (version 1.58.0) RMA method. Ensembl gene ID mappings were retrieved for each probeset using biomaRt (version 2.50.0), Ensembl database (ensembl.org, release 107). Differential expression analysis was performed in R (version 4.1.3) using limma (version 3.50.3); all groups were compared pairwise for each probeset to generate a moderated t-statistic and associated p- and adjusted p-value. Gene annotations were assigned for every probeset that mapped to exactly one Ensembl gene ID using the custom annotation tables generated in-house as detailed in GL-DPPD-7110 (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md</a>), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and org.Dm.eg.db (version 3.15.0).","name":"GeneLab microarray data processing protocol","parameters":[{"@id":"#139758291345120","parameterName":{"@id":"0WRGQg0CQE9po7tFTTxvzgK1MeRbynhW6HAHlILY","annotationValue":"array data file","comments":[],"termAccession":"","termSource":""}},{"@id":"#139758291343680","parameterName":{"@id":"K118AXUyIEG1ZYS51uguXcjP8ntWEkDmw8vHFKwv","annotationValue":"Raw Intensities Table","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139758291344112","parameterName":{"@id":"RpH2RFEgfhHH505JAZKmbs1qSQxqTEWunuvVxI6T","annotationValue":"Normalized Expression Table","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139758291342672","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""}],"publicReleaseDate":"11-Dec-2013","publications":[{"authorList":"Taylor Katherine, Kleinhesselink Kurt, George Michael D., Morgan Rachel, Smallwood Tangi, Hammonds Ann S., Fuller Patrick M., Saelao Perot, Alley Jeff, Gibbs Allen G., Hoshizaki Deborah K., von Kalm Laurence, Fuller Charles A., Beckingham Kathleen M., Kimbrell Deborah A.","comments":[],"doi":"10.1371/journal.pone.0086485","pubMedID":"24475130","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"Toll Mediated Infection Response Is Altered by Gravity and Spaceflight in Drosophila"}],"studyDesignDescriptors":[{"@id":"h0shfCKjUqWbQbBHH9iZLu4lX5tHwbttyXVJiTw5","annotationValue":"transcription profiling by array","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0002768","termSource":"EFO"},{"@id":"G18x8YsiHNJtkVdmhg9hAuzPv2Xvir8TpCqjEpRS","annotationValue":"low Earth orbit","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000019","termSource":"RBO"}],"submissionDate":"10-Dec-2013","title":"Expression data from drosophila melanogaster","unitCategories":[{"@id":"HD9tp2SLnR0wXOGt79HG2Wa7QP9SkYuVwR6aCHGl","annotationValue":"day","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000033","termSource":"UO"},{"@id":"SHRIFGDc50meal3f60aKnlHyc0mXQoqiyW1BovrZ","annotationValue":"milligray","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000142","termSource":"UO"},{"@id":"kQ7xX41a7tbtWDBfRbxYY3YI0jpDae5GiMFij6BD","annotationValue":"milligray per day","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0010063","termSource":"UO"}]}],"version":7}},"success":true}