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Fig. 1 | BMC Genomics

Fig. 1

From: A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

Fig. 1

Schematic representation of the different steps in the data workflow for Illumina bead arrays. Steps 1–5 are part of the newly added Illumina QC and pre-processing module. (1) Import the input data text files; (2) Enter sample annotation and experimental grouping, by either uploading a description file or completing the form (array names are pre-filled based on the data set uploaded); (3) Summary of the array type, species and number of arrays found in the data set and whether data has been background corrected, with an option to enter an email address for notification when the workflow has finished; (4) Select a pre-processing method and the plots and tables to be computed on the raw and pre-processed data; (5) Obtain the normalized data table and diagnostic images to check the data quality. Illustrative examples of such tables and images are shown (array boxplots, array correlation heatmap, head of normalized data table). Optionally, steps 1 to 5 of the pre-processing procedure may be repeated after exclusion of low quality arrays. The output files can be further used to perform statistical analyses through the statistics module and pathway analysis through the pathway analysis module, or to proceed with downstream analyses in external tools

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