[BioC] Reading .bpmap files for homemade tiling arrays

[raphaelgottardo]

Hi Larry and Patrick,

Sorry for the late reply.
Indeed, it is most likely the error that Larry reported. I have included a test to make sure that the groupName is valid. It should appear in the devel version, as  of rMAT 2.5.1. 
If things go well, I will push it to the Branch release next week. It's a minor fix. In the meantime please make sure your groupName is valid. 

Best,

Raphael

On 2010-05-17, at 8:33 PM, Larry Singh wrote:

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.

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