[BioC] Reading .bpmap files for homemade tiling arrays

[Noah Dowell]

Hello Patrick,

I don't know what your setup is but when I am dealing with unknown files then the simple Unix command:

head <filename>

in a terminal window (or Unix interpreter) will give me the top ten lines of the file and then I can figure out what columns I need.
I thought I used that on some bpmap files a while back but maybe I am misremembering.

Also the Ringo and Starr packages have a function to read bpmap files which you could you to read in and then explore the file...

best,

noah


On May 17, 2010, at 5:33 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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