In PgaeMan, I've been successfully mapping Arabidopsis data files using 'Mapping_overview_AgiCode.m02'
Question 1 - what is the origin of this mapping file? Looked for info online but couldn't find any.

I get insufficient memory error when trying to use Ath_AGI_TAIR8.m02 on a 2GB RAM PC desktop.

I get a different error message (-1 in first column) when using Ath_AGI_TAIR9_Jan2010 in either .m02 or .txt form.
Question 2 - Is there a fix available to that mapping file so it can be used in PageMan?

Thanks in advance for advice.

Dear Heidi,

thanks for your interest in PageMan. In order to be able to investigate the problem you are describing, it would be helpful for us
to have some more details. Which version of PageMan are you using and on which operating
system? Are the IDs in your data files TAIR8 oder TAIR9 based. Using MapMan i cannot reproduce the
error message you mention (-1 in first column).

Best greetings,
Marc

Hi Marc,

Thanks for the quick reply. I'm using 0.12 PAGEMAN on a PC running Windows XP with service pack 3.

I've attached the datafile which generates the error message with the TAIR9 mapping file I downloaded yesterday from the MAPMAN site.

I'm not sure whether my IDs are in TAIR8 or TAIR9 or older form. The data is from an old dataset from an Operon Oligo array (v1.0) but in
the process of statistical analysis and annotation the origninal IDs have been updated several times by myself and others..
If you can tell me how to check and/or convert between ID forms, I will do that.

I have been assuming that I should always choose the most current TAIR mapping file because it contains the most up to date functional annotation.

The attached data file is mappable using the older mapping file sent to me by a collaborator Dave Weston, which tells me that PAGEMAN itself is working OK.

Let me know what you find out when you try them.

Thanks, Heidi

Dear Heidi,


1.)
What do you exactly mean by origin of the file Mapping_overview_AgiCode.m02?
Marc may give the iinformation about the underlying TAIR release (My guess is: pretty old one (TAIR 5)!
You may download an up to date mappings (TAIR versions 6 to 9) from the http://mapman.gabipd.org/web/guest/mapmanstore.



2.)
Concerning the memory problem you can allow PageMan to use more memory!
You need to edit the PageMan.lax file which resides within the PageMan Installation directory using the e.g MS Windows Notepad.
Usually (C:\Program Files\PageMan\PageMan.lax)
Add the following two lines which set the maximum allowed memory:

lax.nl.java.option.java.heap.size.initial=209715200
lax.nl.java.option.java.heap.size.max=550000000



And finally, if you are used to the MapMan software you can also try out the new MapMan3.5.0APHA which now contains the PageMan funtionality. The
ALPHA status is due to the fact that we still incorporate some usability enhancements. So the PageMan integration is as stable as the PageMan standalone except that the visualization options have been improved.

have a nice day
Axel

Hi Axel,
Thanks for the quick response.

1.)
What do you exactly mean by origin of the file Mapping_overview_AgiCode.m02?
Marc may give the iinformation about the underlying TAIR release (My guess is: pretty old one (TAIR 5)!
You may download an up to date mappings (TAIR versions 6 to 9) from the http://mapman.gabipd.org/web/guest/mapmanstore.

I did try the up to date mapping first, and the TAIR 9 mapping file is the one that generated an error with the data file (attaached).
That same data file worked with the older mapping, so I know that PAGEMAN itself is working OK.

2.)
Concerning the memory problem you can allow PageMan to use more memory!
You need to edit the PageMan.lax file which resides within the PageMan Installation directory using the e.g MS Windows Notepad.
Usually (C:\Program Files\PageMan\PageMan.lax)
Add the following two lines which set the maximum allowed memory:

lax.nl.java.option.java.heap.size.initial=209715200
lax.nl.java.option.java.heap.size.max=550000000

I tried doing this but it disabled the file and the program. Is there a specific place in the file I should insert those two lines?

And finally, if you are used to the MapMan software you can also try out the new MapMan3.5.0APHA which now contains the PageMan funtionality. The ALPHA status is due to the fact that we still incorporate some usability enhancements. So the PageMan integration is as stable as the PageMan standalone except that the visualization options have been improved.

I would love to try MapMan 3.5.0 ALPHA. I am trying it now.

Thanks, HEidi

Dear Heidi,

I inserted the memory options I gave to you at the top of the file PageMan.lax.
I even copied them from this forum to make sure that there are no problems due to that.
Did you choose the Microsoft Notepad to edit the file?!
A re installation of PageMan 0.12 will overwrite the PageMan.lax file to the original version as I cannot give you a clean version of the file as it is written during installation and contains your install pathes.

I just tried the PageMan 3.5.0ALPA with your data set and AGI mappings tair8 and tair9. I t went fine ;-). It will already allow more memory to be used.
Using PageMan within MapMan differs a bit as it conforms now to the general MapMan way of doing things.

1.) Attach your data file to the left hand tree : File Menu => add Data should do.
2.) right click on the data file and choose show in PageMan, thats all.


Hope you can instantly use MapMan 3.5.0ALPHA.

Axel

Dear Axel,

I did get my data files to work in MapMan 3.5 with TAIR 9 - thanks!

Does MapMan 3.5 have the treatment comparison function that PageMan has, ie table of statistically enriched functions for mutliple treatments?
I'd like to use this function to identify specific pathways to look at in more detail in MAPMAN.
This PAGEMAN function is especially useful because I'm working with plant responses to insects which:
1) are poorly studied and inducing gene expression patterns very different from other better studied plant stresses so I need to discover
any 'new' patterns rather than just those induced by other stresses
2) involve 16 different comparisons (4 insect spp, w time points, different tissue types (attacked and unattacked)) and its more efficient to look
at many of them at the same time at the early 'pattern discovery' stage before I use MAPMAN to look in detail.
So, I'd still like to get my files to work in PAGEMAN with TAIR9 mapping files. CAn you help me with that?

Last, I'll try again to modify the pageman.lax files and I'll put the new lines at the top. My problem may have been in how I save the modified files after editing in WordPad. When I do it again I'll make sure that it is saved as Pageman.lax.

Really appreciating your help!

Heidi

Dear Heidi,

I'm sorry to answer that late.
I hope you have solved the problem starting pageman with more memory.
Nevertheless the problem might have been due to using wordpad instead of notepad.It might add fancy characters which the PageMan installer does not like.

I do not completely understand your question, but as far as I know, all functions of PageMan have been incorporated into the latest PageMan version.
You can add data sets one by one. Just left cklick on the data sets in the left hand tree while havin gthe PageMan like display open in MapMan.

Concerning other questions I will forward your question immediately to the expert.

have a nice day
Axel