[BioC] gcrma output id

[Dianjing Guo]

I just tried with two of my cel files and the results seems to be 
correct. The problem happens only when i try to normalize 60 chips 
together. Does it mean it has limits requirement? Or something is wrong 
with any of my particular cel file?

Thanks,
Dianjing

Zhijin Wu wrote:

>This is surprising since gcrma calls rma after its background correction
>step. Would you provide me your code calling gcrma and maybe one array
>of your data so I can try it?
>
>On Tue, 2 Nov 2004, Dianjing Guo wrote:
>
>  
>
>>i just tried rma and it gives normal affy_id.
>>
>>Dianjing
>>
>>Zhijin Wu wrote:
>>
>>    
>>
>>>Would you do me one favor of trying rma instead of gcrma and see what ids
>>>you get? Thank you! 
>>>
>>>
>>>On Tue, 2 Nov 2004, Dianjing Guo wrote:
>>>
>>> 
>>>
>>>      
>>>
>>>>I get regular yeast affy_ids such as :
>>>>[8440] "9164_at"              "9165_at"              "9166_at"
>>>>[9268] "9992_at"              "9993_at"              "9994_at"
>>>>
>>>>D.
>>>>
>>>>Zhijin Wu wrote:
>>>>
>>>>   
>>>>
>>>>        
>>>>
>>>>>That is strange. GCRMA does not generate its own ids. 
>>>>>What affy ids do you get when you use geneNames(your AffyBatch object)?
>>>>>
>>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote:
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>>
>>>>>          
>>>>>
>>>>>>No that's not the case. I'm using yeast ygs98 chip and the ids should be 
>>>>>>smaller than 9335. But what i got from gcrma are strange ids like 
>>>>>>190400, 189866, 190402 etc.
>>>>>>
>>>>>>Thanks,
>>>>>>Dianjing
>>>>>>
>>>>>>Zhijin Wu wrote:
>>>>>>
>>>>>>  
>>>>>>
>>>>>>       
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>the rownames of exprs(gcrma_output) should be the affy_id 
>>>>>>>
>>>>>>>
>>>>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>    
>>>>>>>
>>>>>>>         
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>>>When i use gcrma to normalize my data, the result output gives id that 
>>>>>>>>doesn't match with affy_id. Anyone can point out how to match the id to 
>>>>>>>>my genes on affy chip?
>>>>>>>>
>>>>>>>>Thanks,
>>>>>>>>Dianjine
>>>>>>>>
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>>>>>>>>Bioconductor mailing list
>>>>>>>>Bioconductor at stat.math.ethz.ch
>>>>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>
>>>>>>>> 
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