Hi Setsuko,

I haven't looked at this in a long time, and I can't seem to find the CDF file 
that I used locally on my computer.  The information regarding the antigenomic 
probesets should be readily available in the files you get from Affymetrix 
though, if you want to custom build a CDF file.

To be honest, when I did this >2 years ago, there was no "official" GCRMA 
implementation for Gene 1.0 ST arrays.  Maybe Bioconductor has this now for 
these arrays?

I've cc'd the aroma.affymetrix mailing list in the hope that someone has a 
better solution for you.


On Jun 21, 2011, at 8:28 AM, Setsuko Sahara wrote:

> Dear Mark
> I found your previous e-mail regarding an application of gcrma to data for 
> Gene ST arrays. Do you happen to have a chance to provide us of antigenomic 
> probesets somewhere? Or do you recommend to try your previous scripts?
> Sincerely,
> setsu
> Mark Robinson
> Sun, 29 Mar 2009 23:12:09 -0700
> Hi Mario.
> I have made some modifications to the reading of probe_tab files and  
> to the computing of affinities so that this procedure can run now,  
> either as you have done below by choosing lowly expressed probes, or  
> (perhaps preferably) by using the 'antigenomic' probes on the array:
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-30); timestampOn(verbose)
> cdf<-AffymetrixCdfFile$fromChipType("HuGene-1_0-st- 
> v1",verbose=verbose,tags="PD")
> cs<-AffymetrixCelSet$fromName("tissues",cdf=cdf,verbose=verbose)
> bcGc <- GcRmaBackgroundCorrection(cs,  
> type="affinities",indicesNegativeControl = negativeControlIndices)
> csGBC <- process(bcGc,verbose=verbose)
> controlIndices <- which(!isPm(cdf))
> bc <-  
> GcRmaBackgroundCorrection 
> (cs,type="affinities",indicesNegativeControl=controlIndices)
> csBC <- process(bc,verbose=verbose,force=TRUE)
> I needed to make a CDF file that contained these antigenomic probesets  
> as they are not present in the binary-converted CDF files I created  
> previously.  I will make available these CDFs once I can test  
> everything.
> Unfortunately, I do not have a good way of testing that my  
> modifications are doing exactly the right thing, as I am also not  
> intimately familiar with the gcrma model/code.  To be honest, I don't  
> know of anyone that has successfully run gcrma on these chips or Exon  
> ST chips, Bioconductor or otherwise.  Do you?  If so, please let me  
> know.
> These changes can be made available in the next release or possibly  
> earlier with a patch, but I just want to test the changes first.
> Cheers,
> Mark
> Setsuko Sahara

Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobin...@wehi.edu.au
e: m.robin...@garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852

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