Affymetrix support

[Jari Häkkinen]

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

[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

[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

[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?

[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.

[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

[Jari Häkkinen]

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

[Jari Häkkinen]

• 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.