[BioC] gcrma output id

[Dianjing Guo]

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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>>>>>>
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