Standard Operating Procedure for MAGIC Tool

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Open MAGIC Tool (using launcher for your operating system, allocating appropriate amount of RAM)

Start a project or load a previous project.

"Add file" or "Add directory" within MAGIC Tool (or move files into project folder outside MAGIC Tool and update project in MAGIC Tool) to get tiff files, gene list, info file, and any expression files to be merged or analyzed.

If starting with tiff files:

• Load images
• Load gene list
• Addressing and gridding
• Manual and/or autoflagging
• Produce expression file (or append column to existing expression file for additional pairs of tiff files)

Average replicates (to average ratios of gene_rep1 and gene_rep2)

Merge other expression files (add columns = additional chips) if necessary; be sure the same steps have been performed to all files being merged.

Log transform

Standardize

Add gene info

Replace names with aliases (to use common gene names during exploration)

Explore data

Think about your goals for clustering - should you? If no, stop. If yes:

• Calculate dissimilarities
• Compute clusters
• Display clusters