Import Illumina Bead Summary(IBS) files as raw data

[Nicklas Nordborg]

The rawest form of raw data generated by the Illumina scanner are the Illumina Bead Summary(IBS) files. Each sub-array can have one or two files (related to the number of "stripes"). The IBS files are simple and have only four columns:

• Illumicode: The ID of the feature. Same as Array_Address_Id in the bgx files, but without 0-padding.
• N: The number of beads
• Mean GRN: Mean intensity
• Dev GRN: Standard deviation of the intensities

In each file there is only one entry for each feature, but the same feature may have an entry in both files. When importing the values for a feature must be merged. The intensity value is simply the weighted (by the number of beads) mean of the values in the two files. The number of beads are simply added. We need to find a formula for how to merge the standard deviation values.

[Nicklas Nordborg]

(In [560]) References #91: Import Illumina scandata files as raw data

A skeleton that installs and compiles.

[Nicklas Nordborg]

(In [562]) References #91: Import Illumina scandata files as raw data

The plug-in can now import data, but error handling is very limited.

[Nicklas Nordborg]

(In [564]) References #91: Import Illumina scandata files as raw data

Error handling is now also in place. There should only be minor bugs and cleanup to do.

[Nicklas Nordborg]

(In [568]) References #91: Import Illumina scandata files as raw data

Call checkInterrupted()

[Martin Svensson]

Changed scandata -> Bead Summary

[Nicklas Nordborg]

(In [588]) Fixes #91: Import Illumina Bead Summary(IBS) files as raw data

[Nicklas Nordborg]

(In [631]) References #91: Import Illumina Bead Summary(IBS) files as raw data

Changed default value for "Missing feature" to skip, since the IBS files seems to have ID:s not appearing in the BGX files.