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ImSig Scoring Algorithm Work Flow

Requirements:

1. P-Data file (Need to be downloaded separately)
2. Transcriptomic data of your samples in log2 scale
3. R software

Preparation of sample file

1. Tab-delimited tabular input format with no double quotations and no missing entries.
2. The expression values must in log2 scale.
3. The first column must contain HUGO Gene Symbols.
4. Gene symbols should not be redundant. Please collapse multiple probes to a single gene by choosing the probe with the highest average intensity across samples.
5. ImSig performs a feature selection and therefore typically does not use all genes in the matrix. It is generally ok if some genes are missing from the user’s transcriptome file. Although it is not recommended to run if the overlap is <75% of signature genes.

An example expression file is shown below.

Running ImSig Algorithm

1. Download Pdata files from: https://github.com/systems-immunology-roslin-institute/ImSig/tree/master/Pdata%20Files
2. Save the expression file along with the Pdata files in a separate folder.
3. Boot R.
4. Install "Plyr" package.
5. Change the working directory to the folder in which the expression file and Pdata files are saved.
6. Run the appropriate R script.