[BioC] gcrma output id

[Zhijin Wu]

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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> >>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>>>
> >>>>>>  
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>    
> >>
> 
>