Opened 15 years ago

Closed 14 years ago

#435 closed defect (fixed)

A check for reporter information is needed when adding/using affymetrix data

Reported by: Jari Häkkinen Owned by: Nicklas Nordborg
Priority: major Milestone: BASE 2.4
Component: web Version: trunk
Keywords: Cc:

Description

Affymetrix data can be used up to the point when a plug-in (RMAExpress) tries to push results into the dynamic tables. At this point the core will throw an exception complaining about missing reporters. The behaviour is assymetric compared to genepix where import of raw bioassays cannot be done if no reporter information is available in the database.

For Affymetrix a similar check should be done, either when creating new raw bioassays or before starting plug-ins.

Change History (8)

comment:1 Changed 15 years ago by Jari Häkkinen

Relates to ticket:372

comment:2 Changed 15 years ago by Nicklas Nordborg

The check would probably have to be done when creating the array design since it is the CDF file that has information about the reporters. The CEL file just contains references to the CDF file. There is a LGPL java package at http://morden.csee.usf.edu/software/ for parsing CDF files in both text and XDA format.

However, checking that the reporters exists when creating the array design is not a guarantee that the reporter will exist when doing the RMAExpress normalisation. There is nothing that prevents that the reporters are deleted in the mean time. In other words, the RMAExpress plugin should never expect that the reporters exists.

comment:3 Changed 15 years ago by Nicklas Nordborg

Milestone: BASE 2.2BASE 2.x+

comment:4 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.x+BASE 2.4

comment:5 Changed 15 years ago by Johan Enell

Owner: changed from Johan Enell to Nicklas Nordborg

comment:6 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.4BASE 2.3

Milestone BASE 2.4 deleted

comment:7 Changed 14 years ago by Nicklas Nordborg

Status: newassigned

comment:8 Changed 14 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [3482]) Fixes #435.

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