I just ran the test file you sent. The file ran fine, but
didn't return a results file since the Other ID is not
informative. It did generate a proper exception file that
indicated no ID was found, as it should. As Kristina
mentioned, to properly use MAPPBuilder (as a precursor for
making an illustrated pathway like those at WikiPathways),
you will need to either have the gene IDs represented in
the GenMAPP database or have the user add these as a
custom database.
> Hello Michal,
> This MAPPBuilder error is usually due to formatting
>problems in the
> input file, such as bad gene IDs or double-quotes in
>label entries. If
> you can send us the whole input file
>(genm...@gladstone.ucsf.edu) we
> can look into it.
> I noticed you are using the system code for Other. This
>category is
> not actually a functioning category in the database in
>terms of
> linking between gene IDs. So if you import expression
>data, or try to
> build a MAPP in MAPPBuilder with this code, the
>resulting genes will
> not link to anything in the database and therefor it
>will basically be
> useless. Do you have any other annotation (Entrez,
>Ensembl) that could
> be used for importing data instead?
> Also, just to clarify, MAPPBuilder is used to import a
>list of IDs as
> a starting point when drawing a new pathway MAPP, to
>avoid having to
> enter many IDs manually in the Gene Finder. If you want
>to import
> array data to visualize on existing pathways, use the
>Expression
> Dataset Manager.
> Regards,
> Kristina
> On Aug 13, 12:10 pm, Michal
><michal.blazejc...@gmail.com> wrote:
>> Hi,
>> Our software package, FlexArray, is capable of exporting
>>data in
>> MAPPBuilder format. Recently one of our users reported
>>that he is
>> unable to import such a file to MAPPBuilder.
>> This is roughly how the file looks like:
>> GeneID SystemCode Label Head Remarks MAPPName
>> OR51L1 O OR51L1 test
>> OR51Q1 O OR51Q1 test
>> ZNF683 O ZNF683 test
>> OR51S1 O OR51S1 test
>> ZNF643 O ZNF643 test
>> ZNF653 O ZNF653 test
>> ZNF663 O ZNF663 test
>> (the gene ids are Illumina target ids).
>> We are always getting the following error:
>> Unexpected error in MakeMapps.
>> Not a valid file name.
>> And then:
>> Run-time error '91'.
>> Object variable or With block variable not set.
>> But the file looks just like the examples on
>>pagehttp://www.genmapp.org/help_v2/MAPPBuilder.htm. the
>>file is located
>> in C:\MAPPBuilder-test.small.txt.
>> Does anyone has an idea of what is happening here?
>> We are using version 2.1 of GenMAPP, by the way.
>> Best,
>> Michal
>> PS. BTW, GenMAPP refuses to install on a 64-bit Windows
>>XP machine.
|
