problem importing raw data file to .gex

[gege]

Hi,
I am trying to use GenMAPP to analyze my array results.
But i m having a problem when i want to convert my raw data file
into .gex, here is the message i got:
the number of values of the application must coincide with the number
of destination fields. Can somebody please help me out with this.
I have another issue, I m using Illumina platform, and it seems that
the annotation file could not provide me a good gene list with a good
gene identifier that GenMAPP requires. In my annotation file, i have
gene identifier that gives me just the number without the 'MGI' code,
so i think it will require me to put MGI in every row of my 45k
genelist (I am working at the probe level which gives me more rows, is
this the best way to work with GenMAPP?). So, can somebody suggest me
what to do in handling my data in order to make it compatible with the
GenMAPP?
Thanks a lot and best regards.
Gege

[Nathan Salomonis]

Greetings Gege,

GenMAPP can directly use Illumina IDs for mouse, where the first
column of your spreadsheet has Illumina IDs and the second has the
system code for Illumina (Il - capital i and lower case L). The error
you are getting sounds like a formatting issue. Try not to include
values in a field with either spaces or commas. Some characters can
cause issues with importing as can cells with no value. If you like,
you can send either the whole dataset you wish to import as a GEX or
the first 15 lines and we can test this for you
(gen...@gladstone.ucsf.edu).

Alternatives to GenMAPP are PathVisio (pathvisio.org) and GO-Elite
(genmapp.org/go_elite). Pathvisio is similar to GenMAPP but is more
advanced in terms of the ability to annotate pathways and visualize
data. It is also associated with GenMAPP and uses the same pathways.
GO-Elite is not a pathway visualization program, but performs pathway
and Gene Ontology over-representation analysis with methods improved
over MAPPFinder and with more updated databases.

Best,
Nathan Salomonis