MAP module

A. Try MAP with the example data


B. Run MAP with your own data

HELP: This tab-delimited text file is expected to be a table with 3 columns: (1) Gene symbols, (2) MS intensities of sample 1 and (3) MS intensities of sample 2. If you are still confused about the input file and its format, just click here testing_data.txt to look at a real instance, or you can refer to the manual section for the detailed instruction.

HELP: How to normalized the input data. By default: Trimmed total count.

HELP: Size of the sliding window to scan the ratio-intensity plot (similar to the M-A plot widely used for microarray data analysis). By default: 400 proteins.

HELP: Step size of the sliding window. By default: 100 proteins.

HELP: The fraction of proteins with the weakest intensity changes of each window used to model technical variations. They are assumed to be predominantly comprised of non-differentially expressed proteins. By default: 50 (values higher than 60 or lower than 30 is not recommended).

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