[BioC] Can't reproduce assessment data included in affycomp package

[Harris A. Jaffee]

On Jul 8, 2011, at 2:36 AM, Rafael Irizarry wrote:
> Philippe,
>
> Thanks for catching this. And sorry it took so long to reply. We have
> been busy fixing the problem. Here is what happened: In 2004 we made a
> change to one of the assessment functions. Specifically, the
> definition of low, medium and high strate changed for the fold change
> assessments. Unfortunately we did not rerun the assessment functions
> on the rma and MAS results to fix the pre-computed assessment included
> in the package. This is why you couldn't reproduce it. The website
> also had a few entries that were run with the old functions. We have
> now re-run the current assessment on everything and changed the
> precomputed assessments in the package.
>
> http://affycomp.jhsph.edu
> is updated.


"Affycomp III" will signal the new page (rather than a cached copy of
the old one).  Also, "The advent of ...", pointing here:

	http://affycomp.jhsph.edu/AFFY3/II_to_III.html

> You can see the old ones here:
> http://affycomp.jhsph.edu/AFFY2/TABLES.hgu/0.html

and for historical purposes,

	http://affycomp.jhsph.edu/AFFY2/comp_form.html

> Fortunately, things don't change much.
>
> The affycomp package now contains all the new assessments. Those that
> have been comparing  a method to the rma or MAS 5.0 precomputed
> assessment should re-run the comparison.

A new comparison tool is available here:

	http://affycomp.jhsph.edu/AFFY3/comp_form.html

> Sorry for any trouble this caused.
>
> Best wishes,
> Rafael
>
> On Wed, Apr 20, 2011 at 1:57 AM, Philippe Serhal
> <philippe.serhal at umontreal.ca> wrote:
>> I can't quite seem to reproduce the precomputed MAS 5.0 and RMA
>> assessments provided in the affycomp package.  Although I have been
>> unable to find the code that was originally used to generate them, I
>> think it is fairly safe to assume it looked a little something  
>> like this
>> (given a current working directory containing the HG-U133A spike- 
>> in data
>> [1]):
>>
>> R> library (affy)
>> R> library (affycomp)
>> R> data <- ReadAffy ()
>> R> eset <- rma (data)
>> R> write.table (data.frame (2 ^ exprs (eset), check.names = F),
>>  + file = "tmp.csv", sep = ",", col.names = NA, quote = F)
>> R> tmp <- read.newspikein ("tmp.csv")
>> R> a <- assessSpikeIn2 (tmp, method.name = "RMA_testing")
>>
>> I then compare this with the precomputed assessments:
>>
>> R> data (rma.assessment2.133)
>> R> affycompPlot (rma.assessment2.133, a)
>>
>> Four of the six resulting figures [2] -- 1b, 2b, 4c, and 5e -- show
>> identical results for the two assessments, while the other two --  
>> 5c and
>> 5d -- show significantly diverging results.  Thinking perhaps the
>> assessments had been computed using an older version of RMA, I tried
>> 'bgversion = 1' in the rma() call, but that didn't help.  In fact,  
>> this
>> doesn't seem to have anything to do with the RMA pipeline, because  
>> if I
>> repeat the process substituting 'mas5' for 'rma' and
>> 'mas5.assessment2.133' for 'rma.assessment2.133' (and not
>> exponentiating), I obtain similar results: 5c differs, but none of  
>> the
>> others.
>>
>> Any idea what I'm doing wrong here?  Thank you in advance for any
>> insight you may be able to provide.
>>
>> R version: 2.10.0
>> affy version: 1.24.1
>>
>> [1] HG-U133A spike-in data:
>> http://www.biostat.jhsph.edu/~ririzarr/affycomp/hgu133spikein.tgz
>> [2] affycomp figure definitions:
>> http://affycomp.jhsph.edu/AFFY2/comp_form.html#definitions
>>
>> --
>> Philippe Serhal
>> Functional and Structural Bioinformatics Lab
>> Institute for Research in Immunology and Cancer (IRIC)
>> Université de Montréal
>>
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