NF_MAAffymetrix_1.0.3 generate_protocol.sh update

- Replaced stub link with release link

Author: torres-alexis

Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/modules/POST_PROCESSING/GENERATE_PROTOCOL/resources/usr/bin/generate_protocol.sh

@@ -58,7 +58,7 @@ else
 fi
 
 # Read the template file
-template="Data were processed as described in GL-DPPD-7114 (https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md) using NF_MAAffymetrix version 1.0.3 (GitHub link coming soon).  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 ${dp_tools_VERSION}). The raw array data files were loaded into R (version ${R_VERSION}) using oligo (version ${oligo_VERSION}). Raw data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version ${oligo_VERSION}). The raw probe level intensity data was background corrected and normalized across arrays via the oligo (version ${oligo_VERSION}) quantile method. Normalized probe level data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version ${oligo_VERSION}).  Normalized probe level data was summarized to the probeset level using the oligo (version ${oligo_VERSION}) RMA method. ${GENE_MAPPING_STEP} Differential expression analysis was performed in R (version ${R_VERSION}) using limma (version ${limma_VERSION}); 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 (https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and ${GENE_ANNOTATION_DB} (version 3.15.0)."
+template="Data were processed as described in GL-DPPD-7114 (https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md) using NF_MAAffymetrix version 1.0.3 (https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.3/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix).  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 ${dp_tools_VERSION}). The raw array data files were loaded into R (version ${R_VERSION}) using oligo (version ${oligo_VERSION}). Raw data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version ${oligo_VERSION}). The raw probe level intensity data was background corrected and normalized across arrays via the oligo (version ${oligo_VERSION}) quantile method. Normalized probe level data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version ${oligo_VERSION}).  Normalized probe level data was summarized to the probeset level using the oligo (version ${oligo_VERSION}) RMA method. ${GENE_MAPPING_STEP} Differential expression analysis was performed in R (version ${R_VERSION}) using limma (version ${limma_VERSION}); 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 (https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and ${GENE_ANNOTATION_DB} (version 3.15.0)."
 
 # Output the filled template
 echo "$template" > PROTOCOL_GLmicroarray.txt