[BioC] combine pm and oligo sequence information

[James W. MacDonald]

Wang, Yonghong (NIH/NCI) wrote:
> Jim: Thanks for the help. It works, and I really love the result. Another
> question related to the original one is about the pm value. I am wondering
> whether the pm value generated using function pm() are already background
> subtracted (same as the method "mas"). If not, how can I subtract the noise
> level background (not MM background) of each spot from affy chip? Thanks a
> lot for the help.

The PM values you are extracting are not background corrected. You can 
see the available methods for background correction by typing 
bgcorrect.methods at an R prompt (after loading the affy package).

 > bgcorrect.methods
[1] "mas"  "none" "rma"  "rma2"

If you want the background corrected values:

abatch <- bg.correct(abatch, "rma")

Where abatch is the name of your affybatch (which I am sure is no longer 
'data' ;-D).

Then run the rest of the code as before.

> By the way, I really like the bioconductor mailing list and have joined
> after I submitted my first question a few days ago. I am not quit sure
> whether I should also submit this follow-up question to the mailing list.
> But I will do so next time.

Yes. All followup questions should also go to the list, so others can 
use the list as a reference for questions that may have already been 
answered.

Best,

Jim



> 
> Thanks
> Yonghong
> 
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: Thursday, June 16, 2005 3:15 PM
> To: Wang, Yonghong (NIH/NCI)
> Cc: 'bioconductor at stat.math.ethz.ch'
> Subject: Re: [BioC] combine pm and oligo sequence information
> 
> Wang, Yonghong (NIH/NCI) wrote:
> 
>> >i.pm <- indexProbes(data, "pm");
>>
>>
>>
>>>xy.pm <- indices2xy(i.pm, abatch = data);
>>
>>
>>>seq.pm <- u133x3pprobe$RESIDUES[(xy.pm[,1] == u133x3pprobe$POSITIONX +1)&
>>
>>(xy.pl[,2] == u133x3pprobe$POSITIONY + 1)];
> 
> 
> 
> i.pm <- unlist(indexProbes(data, "pm"))
> ## note here that 'data' is a poor choice for a variable name
> ## you are masking an existing function. dat or Data would be better
> 
> ## convert X and Y values to indices
> i.pt <- xy2i(u133x3pprobe$x, u133x3pprobe$y)
> ## match the affybatch order to the probe table order
> index <- match(i.pm, i.pt)
> ## extract sequence
> seqnc <- u133x3pprobe$sequence[index]
> write.table(cbind(probeNames(data),pm(data),mm(data), 
> seqnc),file="mytest.dat",sep = "\t")
> 
> HTH,
> 
> Jim
> 
> 
> 
>> 
>>
>>Y. Wang
>>
>>ATC/NCI/NIH
>>
>> 
>>
>>
>>	[[alternative HTML version deleted]]
>>
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>>Bioconductor at stat.math.ethz.ch
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> 
> 
> 


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623