[BioC] AffyBatch to ProbeSet? SpikeIn and Hgu-133?

[Mohammad Esad-Djou]

Thanks for your answer. It helped me.  

For 2. question: I would like to use HG-U133ATAG. 
> > 2. Relationship between SpikeIn and Hgu-133 is unclear to me.  Can someone explain to me? Is there literature in addition?
> > 
> 
> The HG-U133A is an Affymetrix chip whereas the Spike-in could be one of 
> two experiments that were run by Affymetrix using HG-95A and HG-U133ATAG 
> chips. I doubt that answers your question, but I am not sure exactly 
> what you are trying to determine. Can you rephrase the question?

I have a small program, which runs with "SpikeIn" in affy Package without errors: (R Ver. 2.0.1) and 
SpikeIn: 
ProbeSet object:id=AFFX-BioB-5_at
pm= 20 probes x 12 chips

my program:

data(SpikeIn)
pms <- pm(SpikeIn)
mms <- mm(SpikeIn)
concentrations <- matrix(as.numeric(sampleNames(SpikeIn)), 20, 12, byrow = TRUE)

par(mfrow = c(1, 2))
matplot(concentrations, pms, log = "xy", main = "PM", ylim = c(30,20000))
lines(concentrations[1, ], apply(pms, 2, mean), lwd = 3)
matplot(concentrations, mms, log = "xy", main = "MM", ylim = c(30,20000))
lines(concentrations[1, ], apply(mms, 2, mean), lwd = 3)


Now I would like to run same test with HG-U133ATAG. 
I downloaded the file of HG-U133A_tag_description.zip.
(http://www.affymetrix.com/support/technical/sample_data/datasets.affx)   

Now my questions:  

1. Gor I correct file?  

2. how can I use above program for HG-U133ATAG?

Best regards,
Mohammad Esad-Djou

"James W. MacDonald" <jmacdon at med.umich.edu> schrieb am 12.05.05 19:27:24:
> 
> Mohammad Esad-Djou wrote:
> > Hello, 
> > 
> > 1. I would like to convert Hgu-133 experiment from AffyBatch to ProbeSet.  Is it possible ?  If yes, how?
> 
> Well, if you mean the ProbeSet class, then you would use the probeset() 
> accessor function. If you simply want all the probes for each probeset 
> in e.g., a list, you would use probes(abatch, LISTRUE=TRUE). Note that 
> you will have to extract the PM and MM data separately.
> 
> > 
> > 2. Relationship between SpikeIn and Hgu-133 is unclear to me.  Can someone explain to me? Is there literature in addition?
> > 
> 
> The HG-U133A is an Affymetrix chip whereas the Spike-in could be one of 
> two experiments that were run by Affymetrix using HG-95A and HG-U133ATAG 
> chips. I doubt that answers your question, but I am not sure exactly 
> what you are trying to determine. Can you rephrase the question?
> 
> Best,
> 
> Jim
> 
> 
> > Thanks,
> > Mohammad Esad-Djou
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> 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