Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#91 closed task (fixed)

Import Illumina Bead Summary(IBS) files as raw data

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Illumina package v1.0
Component: net.sf.basedb.illumina Keywords:
Cc:

Description (last modified by Martin Svensson)

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.

Change History (9)

comment:1 Changed 12 years ago by Johan Enell

Milestone: Illumina package v1.0

comment:2 Changed 12 years ago by Nicklas Nordborg

Owner: changed from Johan Enell to Nicklas Nordborg
Status: newassigned

comment:3 Changed 12 years ago by Nicklas Nordborg

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

A skeleton that installs and compiles.

comment:4 Changed 12 years ago by 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.

comment:5 Changed 12 years ago by 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.

comment:6 Changed 12 years ago by Nicklas Nordborg

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

Call checkInterrupted()

comment:7 Changed 12 years ago by Martin Svensson

Description: modified (diff)
Summary: Import Illumina scandata files as raw dataImport Illumina Bead Summary(IBS) files as raw data

Changed scandata -> Bead Summary

comment:8 Changed 12 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

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

comment:9 Changed 12 years ago by 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.

Note: See TracTickets for help on using tickets.