[BioC] gcrma with bpmap file instead of cdf file

[Baoqiang Cao]

Hi Kasper,

Thanks a lot for your reply!

Yes, I am using gcrma to run a background correction for tiling array data. 

"And that should be possible witha  bit of hand-tweaking I _think_."

Would you please show me any instruction on that then? 

Thanks again!

Best,
 Baoqiang


---- Original message ----
>Date: Thu, 11 Jan 2007 08:42:25 -0800
>From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>  
>Subject: Re: [BioC] gcrma with bpmap file instead of cdf file  
>To: caobg at email.uc.edu
>Cc: bioconductor at stat.math.ethz.ch
>
>It depends on what you mean with gcrma. I assume you are using a  
>tiling array since you have bpmap files. On a tiling array there are  
>not really any probesets, which is required by parts of gcrma.
>
>What you might be interested in is running the background correction  
>as well as the normalization. And that should be possible witha  bit  
>of hand-tweaking I _think_.
>
>Kasper
>
>On Jan 10, 2007, at 8:39 AM, Baoqiang Cao wrote:
>
>> Dear All,
>>
>> I'm trying to use gcrma to analysis the data I have. Unfortunately,  
>> I only have cel file and the bpmap file for the arrays. It seems  
>> that cdf file is manditory for gcrma, any possibile way I could  
>> bypassing it with the bpmap file? Any help will be certainly  
>> appreciated.
>>
>> Best,
>>  Baoqiang Cao
>>
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