Hi James,

Best to keep this on the list...

That's the code I developed with my old post-doc advisor :) Basically, it 
just pulls out the PM probe names (e.g., "_at1", "at2") and then separates 
them into two columns, one with the probeset name, one with the individual 
probe number. You can then append these to whatever background corrected, 
normalized (or not) pm values, and output the file, which we used to then 
input into SAS for a probe-level analysis. If you want summarized values, 
both 'rma" and 'gcrma' have options to turn off the normalization, and 
'rma' can also turn off the background correction. You can process the 
probe-levels values how ever you like, then get the median polish 
summarization by calling:

my.summarized <- rma(processed.AffyBatch, background=T, normalize=F)

Cheers,
Jenny



At 11:45 AM 12/7/2006, James Anderson wrote:
>Jenny,
>   Thanks for your email. Yeah, you are right, I used the wrong terminology.
>   Below is the R code I downloaded from one uiuc website.
>
>library(affy)
>setwd("C:/test")
>
>rawdata<-ReadAffy()
>PM<-probes(rawdata,which="pm")
>AffyInfo<-dimnames(PM)[[1]]
>cutpos<-regexpr("\\d+$",AffyInfo,perl=T)
>AffyID<-substr(AffyInfo,1,cutpos-1)
>probe<-as.numeric(substr(AffyInfo,cutpos,nchar(AffyInfo)))
>data.bgc<-bg.correct(rawdata,method="rma")
>data.bgc.q<-normalize.AffyBatch.quantiles(data.bgc,type="pmonly")
>pm.bgc.q<-probes(data.bgc.q,which="pm")
>normalized<-cbind(AffyID,probe,pm.bgc.q)
>write.table(normalized,file="NormalR.csv",sep=",",row.names=FALSE,quote=FALSE)
>
>Do you know how to combine the expression value from the 11 probe into the 
>expression value for one probeset?
>
>   Thanks,
>   James
>Jenny Drnevich <drnevich@uiuc.edu> wrote:
>Hi James,
>
>See 'justRMA' - this was developed to help with the memory limitation
>issues. You really should give the codes you used that led to the error
>message, plus the output of 'sessionInfo()' for us to be able to help you
>better. For example, the output of 'rma' should only give one value per
>probeSET, which is composed of 11 probes, in Affy terminology. That you
>said you are getting 11 lines for each "individual probe" (probeset, I
>assume?) means that you were not calling the right function. What was the
>code you used that supposed led to 11 values after 'rma'?
>
>Cheers,
>Jenny
>
>At 08:55 AM 12/7/2006, James Anderson wrote:
> >Hi,
> > I have about 53 cel files, each one has the size of about 12-13 mega
> > bytes with 22625 probes. I am using affycoretools to do rma, but it
> > complains that the maximum size of memory has been reached. My PC is
> > Windows XP with 2G RAM. Below is the error information.
> >
> >Error: cannot allocate vector of size 209906 Kb
> >In addition: Warning messages:
> >1: Incompatible phenoData object. Created a new one.
> > in: read.affybatch(filenames = filenames, phenoData = phenoData)
> >2: Reached total allocation of 1024Mb: see help(memory.size)
> >3: Reached total allocation of 1024Mb: see help(memory.size)
> >
> >Since RMA is an across sample normalization, and I need to analyze all the
> >53 samples together, I can not separate them into several pieces and then
> >do RMA, MAS5 can do that, but the expression value obtained by MAS5 is not
> >as good as that of RMA. Does anybody know how to solve this problem? In
> >addition, it seems that the output of rma in affy package (not
> >affycoretools) has several lines for each individual probe (my case is 11
> >lines for each individual probe), while the rma in affycoretools directly
> >gives the final expression value for each probe, could anybody tell me how
> >to make the two results from affy and affycoretools comparable with each
> >other?
> >
> >Thanks a lot!
> >
> >James
> >
> >
> >---------------------------------
> >
> > [[alternative HTML version deleted]]
> >
> >_______________________________________________
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>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich@uiuc.edu
>
>
>
>Want to start your own business? Learn how on 
><http://us.rd.yahoo.com/evt=41244/*http://smallbusiness.yahoo.com/r-index>Yahoo! 
>Small Business.

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@uiuc.edu 
	[[alternative HTML version deleted]]

