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

[James MacDonald]

1.) The file you downloaded only tells you the Affy probe ids that
correspond to the mRNA spiked in, and the amount spiked. You will also
need the celfiles (a 141 Mb download).

2.) See ?probeset for information on how to extract ProbeSet objects.

Jim



>>> "Mohammad Esad-Djou" <shahrgol at web.de> 5/13/2005 8:38:27 AM >>>
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
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > 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


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