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4.12. To see what obstacles may arise in the course of loading mapping data, let's try another file. This one, named 'duplicate_mapping_file_tutorial.CSV', will replace the one we loaded in steps 26 to 28 4.5 to 4.6. A partial screenshot of this file, taken from a Microsoft Excel 2007 window, is shown below.

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In this mapping file, the same sample (ID 191) is mapped twice, once to subject ID 5085 (highlighted in red) and again to subject ID 6000 (highlighted in blue).

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Surprisingly, when we repeat the procedure for loading mappings with the 'duplicate_mapping_file_tutorial.CSV', caIntegrator does not display any error message, and the source's status shows as 'Ready to be loaded' in the 'Genomic Data Sources' table, as was the case with the previous mapping file we loaded successfully. Does this mean that caIntegrator allows multiple mappings of the same sample to different subjects?

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When loaded an invalid mapping file, caIntegrator does not display any error messages and shows the status of the invalidly mapped source as 'Ready to be loaded' (highlighted in red).

As it turns out, when caIntegrator parses a mapping file where the same sample is mapped to multiple subjects and encounters a sample ID that has already been mapped, it will overwrite the old mapping with the new one. We can confirm this by clicking on the 'Map Samples' button for the source we mapped and examining the 'Samples Mapped to Subjects' table on the 'Edit Sample Mappings' page.

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On the 'Edit Sample Mappings' page, sample ID 191 is only mapped to a single subject (highlighted in red), even though the mapping file we just loaded mapped that same sample twice.

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We've learned a valuable lesson from this exercise: be sure to check your mapping file for any duplicates before loading it into your study, as caIntegrator does not perform this check for you!