I have tried the catma mapping without succes.
Am I supposed to use the AGI codes as identifiers?
If so what is the difference from using the AGI mapping?
If I should use the AGI codes, whats your recomendation for teh duplicates?
About 3000 CATMa IDs are mapping to a AGI code that can be mapped to at least one other CATMA ID.

Hi,

no actually the CATMA mapping should support the CATMA ids like this CATMA1a11040 which is whatI got from the CATMA people (thanks to them again). If you open your Catma MappingFile you should also see them like this:
CATMA1a11040
At1g12000->...
If these ids is what is beeing used, it might be due to case-sensitivity. MapMan would consider CATMA1a11040 and catma1A11040 to be different items.

Otherwise maybe you can supply me with a typical CATMA array file and I try to fix it.

Thanks for the report
Cheers,
Bj

How,
I actually did not expected respoce this fast - thanks. During the night I have been working a bit more with the data. Yes the proplem was the case of the ID. It works briliantly!
However my question persits. How are the dulplicates treated. I mean the case when two probes (spots) are giving the result for one gene? is Mapman averaging or throwing out one randomly or selecting the highes M value or?
I have been working with the catma platform for abot six monts now and the duplicates are good for many things however they are causing problems with GO and Mapman.

thanks
Johannes

Hi,
MapMan can't deal with duplicated ids,
but if there are two ids for one Gene, they would both be displayed. Actually, these duplicates do pose a big viusal problem, and I guess they should be averaged where possible. I do have a script that does that automatically (if duplicates are known) and furthermore we are currently devloping a preprocessor tool based on BioConductor which would normalize, call DE genes and these kind of things and then would generate a MM output where we could then intercept duplicates.
(On the other hand, if both probes for one gene do go up, it is more reliable to go up then if there was only one probe, so there is some merit in them)
(Also a reason why the CATMA is flagged as experimental)

If your problem is imminent now, just write me an email and we can see together what to do with your samples.
usadel #at #mpimp-golm.mpg.de

Cheers,
Bj