Human Exon 1.0 ST arrays

[Maria Traka]

I've used GenMAPP before for my U133Plus2.0 Affy array data and had
good results but i have now moved to the Affy exon 1.0 ST arrays.
After i summarise my data into gene clusters (transcript clusters) I'd
like to use that in GenMAPP. I tried using the Entrez Gene ID or the
RefSeq ID as the System code but I have three problems; (1), there are
some missing IDs for the genes (which i guess I can't do anything
about), (2), some summarised clusters contain multiple IDs all
separated by /// (e.g. 51750 /// 8771), which gives error messages and
ignores data, and (3) Entrez Gene IDs don't always start with NM_xxxx
(e.g. AF086561 /// BC010942 /// BC063853 /// NM_000019).
Any suggestions? Or maybe plans to incorporate the Transcript Cluster
ID as another Affy System code?

Thanks,
Maria

[GenMAPP Support]

Hi Maria,

The missing genes during import are most likely due to IDs not yet
included in our database, or outdated IDs in the array annotation. For
the clusters with multiple IDs separated by ///, these will need to be
separated out for GenMAPP to understand it. You could do this with a
script. Let me know if you need help with this.
Finally, the Entrez gene IDs should be numerical only, the IDs you
refer to are all GenBank, which are not accepted in GenMAPP. Try to
switch to Entrez gene IDs.

Future versions of GenMAPP will support the exon array directly, but
this will not happen for a while.

Kristina