[BioC] Reading .bpmap files for homemade tiling arrays

[Larry Singh]

Patrick Schorderet <patrick.schorderet at ...> writes:

> 
> 
> Hello everybody,
> 
> I am trying to normalize some ChIP-chip data using rMAT and to do so,  
> you have to feed your .bpmap to the program (the file contains  
> information relating to the design of the Affymetrix tiling arrays).  
> Unfortunately, I get an error saying I am working with doubles instead  
> of the wanted integer. I have not changed the .bpmap file at all and I  
> can make no sense of it because have nothing to open it properly. I  
> guess it might be due to the customized array we are using. The sizes  
> might be different?
> 
> Thanks for the help,
> 
> Patrick

[ ... deleted ]

Patrick,

I had a similar problem, and after some debugging I discovered that you must 
enter a valid groupName when calling BPMAPCelParser.  You can get a list of the 
group names in the bpmap file by just looking at bpmapA$GroupName.  I'm not 
sure this will solve your problem but perhaps it will.

Hope this helps,
-Larry.