Opened 16 years ago

Closed 15 years ago

#150 closed task (fixed)

Affymetrix support

Reported by: Jari Häkkinen Owned by: Jari Häkkinen
Priority: major Milestone: BASE 2.0
Component: coreplugins Version: trunk
Keywords: Cc:

Description


Change History (13)

comment:1 Changed 16 years ago by Jari Häkkinen

Status: newassigned

comment:2 Changed 16 years ago by Nicklas Nordborg

Component: webcoreplugins

comment:3 Changed 16 years ago by Nicklas Nordborg

Milestone: BASE 2.0 RC2BASE 2.0

comment:4 Changed 16 years ago by Nicklas Nordborg

Priority: majorcritical

comment:5 Changed 16 years ago by Jari Häkkinen

Information regarding Affymetrix in BASE 2 is available here: source:trunk/doc/affymetrix.txt

comment:6 Changed 15 years ago by hb[at]stat.berkeley.edu

Just want to drop a note. We've been implementing affxparser in R based on the Fusion SDK (currently v1.0.6). We read CDF, CEL, BPMAP/TPMAP files and the code works on Linux, Solaris, MacOS and Windows. Fusion SDK is fast and has a united API for reading files in ASCII, binary and the new Calvin format. We are really happy with the reader part of the Fusion SDK API and the feedback we get from the Affy people when we need updates. We have just recently started to look into writing/updating Affymetrix files, and our initial feeling is that Fusion SDK has not progressed that far when it come to writing as for reading. I've also seen notes on Affy Devnet that they are lagging behind in the Java version of Fusion SDK.

Cheers

Henrik Bengtsson

comment:7 Changed 15 years ago by Nicklas Nordborg

Summary: Affymtrix supportAffymetrix support

comment:8 Changed 15 years ago by Nicklas Nordborg

(In [2384]) References #150: Affymetrix support It is now possible to link CDF files with array designs. Added icons and functionality for view/download of files without having to go through the file manager

comment:9 Changed 15 years ago by Nicklas Nordborg

(In [2392]) References #150: Affymetrix support Changes to RawDataType? to allow types which stores data in files => Lots of downstream changes to plot functions, filter functions, etc. Allow CEL files to be connected to RawBioAssay?

comment:10 Changed 15 years ago by Jari Häkkinen

An experimental plug-in for computing expression values from uploaded cel files is available at http://baseplugins.thep.lu.se/browser/trunk/se/lu/thep/affymetrix. I'll improve the docs for using the plug-in. The plug-in is not yet available on the demo server.

Improvements needed:

  • The resulting expression matrix is not accessible as a file.
  • Add a browse feature for definition of the underlying RMAExpressConsole binary.
  • The import of the resulting expression matrix is painstakingly slow.
  • The plugin is an INTENSITY type plug-in. Is this the preferred type?
  • More testing.

comment:11 Changed 15 years ago by Jari Häkkinen

A note to Henrik Bengtsson.

We would be interested in hearing about your experience using the Fusion SDK. We'll make contact after the holiday season.

Jari

comment:12 Changed 15 years ago by Jari Häkkinen

Priority: criticalmajor

The RMAExpress plug-in for BASE is release now as version 0.1. It is available through the download section at http://baseplugins.thep.lu.se/. There are some issues left:

  • The resulting expression matrix is not accessible as a file. Should be accessible as a file?
  • The import of the resulting expression matrix is painstakingly slow ... but it works ;-)
  • The plugin is an INTENSITY type plug-in. Is this the preferred type?

This ticket will not be closed until the above issues are considered. Please try the plug-in and provide feedback either through comments here or the ticketing system at http://baseplugins.thep.lu.se

comment:13 Changed 15 years ago by Jari Häkkinen

Resolution: fixed
Status: assignedclosed
  • The resulting expression matrix is still not available as a file and will not be until someone show interest on having it.
  • Import speed has increased and is now in par with the rest of the imports.
  • The plug-in must be an INTENSITY type plug-in.

Please use the BASE mailing lists or the ticketing system at http://baseplugins.thep.lu.se for feedback.

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