Just finished a comparative array study and want to use PageMan to compare bins between species. I can only get Arab (affy ATH1) to work and not G.max. I even used the same G.max mapping (affy) that you created for MapMan. Am I doing something wrong or is this not supported? Thanks for your time.

Dear David,

it would be great if you could specify the problem a bit more - what exactly does not work? Does PageMan crash, possibly displaying an error message? Does the G.max mapping you are using work as expected in MapMan? etc. All these details might help us to pin down your problem. One possible cause might be a case mismatch in your G.max data file and the mapping file. Older versions of PageMan need the identifiers in the data file and the mapping to be exactly the same. If the data file contains probe set identifiers in upper case and the mapping in lower case, PageMan will not be able to map the probe sets to bin and hence do nothing. You can check the case of the IDs in the mapping by simply opening the G.max affy mapping in MapMan.

I hope this helps,
cheers,
Marc

thanks Marc,

The mapping files that I am using were downloaded from the MapMan site and work just fine in MapMan using our data files. I have been using your G.max, Poplar, and Arabidopsis mappings. Arabidopsis works just fine, but both poplar and G.max don't. I am able to load the datafiles, and after I load the mapping nothing happens. In one case I waited 3 hrs just to make sure I wasn't rushing anything.

as you mentioned, there was a case mismatch in the mapping and our datafile for G.max (affy), and I believe that I fixed that and it still didn't work. Let me know if there is anything else to try on the mismatch. There is also mismatch in Poplar but I didn't correct that yet, just G.Max for now.

I am using the Mac OSX 10.5.8 and the latest PageMan version. thanks again for your help.

Dear David,

I'm sorry for the current sluggish response.
Lot's of people are currently ill.
Could you send me an excerpt of your data via email.
That way I could try to find the problem.

Regards
Axel

Marc and Axel,

Thanks for the help. apparently is was simply a RAM issue. I had to run PageMan on a workstation to do among species comparisons. Worked great and more people should use PageMan in my opinion. Not sure why I never had a memory error. Thanks again for the great program and support.