Problem importing data into MAPPBuilder

[Michal]

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 page
http://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.

[Kristina Hanspers]

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 (gen...@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

[GenMAPP]

Hi Michal,

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.

Please email us if you have any more questions.

Best,
Nathan Salomonis