Opened 12 years ago

Closed 11 years ago

Last modified 11 years ago

#100 closed enhancement (fixed)

Add Illumina SNP platform to the installation program

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

Description (last modified by Nicklas Nordborg)

We now have a bit more information about the Illumina SNP platform. It should be a file-only platform. The array design needs manifest files which are similar to the BGX files used in the expression platform. A manual step is needed to create the manifest files. Start with a BPM file and open it in BeadStudio?. Save the file as a csv file. See #93.

Raw data comes from Beadstudio and there are several data sets in a single file. A custom plug-in will use the original file, create one raw bioassay for each data set and then split the original file into one file with data for a single data set in it. See #101.

So, the installation program needs to create:

  • A file-only platform variant, the idea is that this should be a 3-channel data type
  • A new data file type for the manifest files (linked with array design, required)
  • A new data file type for the original data file (linked with raw bioassay, optional)
  • A new data file type for the split data file (linked with raw bioassay, required)

Change History (7)

comment:1 Changed 12 years ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 12 years ago by Nicklas Nordborg

Priority: majorblocker

comment:3 Changed 12 years ago by Nicklas Nordborg

Milestone: Illumina package v1.xIllumina package v1.0
Priority: blockercritical

comment:4 Changed 12 years ago by Martin Svensson

Owner: changed from Johan Enell to Martin Svensson
Status: newassigned

comment:5 Changed 12 years ago by Martin Svensson

(In [589]) References #100 Installation is now including SNP platform-variant and data file types but metadata-extractor and validator are not being set for the data file types. Depends on #93 New SNP-specific columns have been added to extended-properties.

comment:6 Changed 11 years ago by Martin Svensson

Resolution: fixed
Status: assignedclosed

(In [623]) Fixes #100. Add Illumina SNP platform to the installation program

comment:7 Changed 11 years ago by Nicklas Nordborg

(In [626]) References #89, #100: Added formulas for better SNP gui. Gtype = ch(1), Log R Ratio = ch(2), B Allele Freq = ch(3)

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