Hi Elai/Zaid.
You'll want to be careful with all this (i.e. linear models on
unnormalized data ... or maybe you are standardizing some other way),
but yes you can run the probe level model fits on any AffymetrixCelSet
object.
The standard RMA procedure would BG adjust, then quantile normalize,
then fit the PLMs:
cs <- AffymetrixCelSet$byName("BCGC_2006", cdf=cdf)
bc <- RmaBackgroundCorrection(cs, tag="coreR2")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
You could replace this simply with:
csX <- AffymetrixCelSet$byName("BCGC_2006", cdf=cdf)
[...maybe do something else to csX...]
plmTr <- ExonRmaPlm(csX, mergeGroups=TRUE) # put in the
AffymetrixCelSet here you want to fit PLM on
fit(plmTr, verbose=verbose)
Cheers,
Mark
On 30-Nov-09, at 3:32 PM, davic...@gmail.com wrote:
> Henrik
> Is it possible to use aroma to run an RMA implementation without
> quantile normalization? Zaid- have you tried this?
> Best,
> Elai
> CSO
> GenomeDx Biosciences
>
> On Nov 28, 5:51 am, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>> Hi Zaid,
>>
>> I think you have mistaken the aroma.affymetrix mailing list as
>> being a
>> mailing list for Affymetrix software - this forum is only for
>> aroma.affymetrix related topics. Please use the appropriate official
>> Affymetrix forum for their APT software:
>>
>> https://www.affymetrix.com/community/forums/index.jspa
>>
>> That way you also know you will get the correct answer from the
>> correct source. Your question might even have been answered there
>> before (I don't know).
>>
>> /HenrikOn Thu, Nov 26, 2009 at 9:22 PM, zaid <z...@genomedx.com>
>> wrote:
>>> I tried running the 64 bit version of the command tool apt. I was
>>> not
>>> able to find any information to run the command with no
>>> normalization.
>>
>>> I tried many different commands such as: apt-probeset-summarize -a
>>> rma-
>>> bg,pm-only,sea
>>
>>> Any ideas on how I can run that tool with no normlization.
>>
>>> Thanks
>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run
>>> the latest version of the package, 2) to report the output of
>>> sessionInfo() and traceback(), and 3) to post a complete code
>>> example.
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>
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
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