[BioC] Imitating Affy's own steps

[Henrik Bengtsson]

I won't answer you question, because I don't know the answer, but I'd
like to add that there are a few methods out there with the same
names/labels.   I don't know of many carefully done studies showing
that the are numerically or near-numerically reproducible.  If any
know of such, please share them here.  Though I recently discovered:

Christian Stratowa, Introduction to the xps Package: Comparison to
Affymetrix Power Tools (APT), April, 2010 (vignette of the xps
package)

which seems to do a quite serious assessment of the methods
implemented in the xps package - it includes a comparison of
Affymetrix's MAS5.0 implementation with that of the xps package and
the affy package.

/Henrik

On Mon, Apr 12, 2010 at 9:22 AM, Timothy Wu <2huggie at gmail.com> wrote:
> On Mon, Apr 5, 2010 at 10:24 PM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
>
>> Hi Timothy,
>>
>> AFAIK, you have two choices. Using the affy package, you can use mas5() and
>> mas5calls(). You can also use justMAS() from the simpleaffy package.
>>
>> I don't believe either one will give you exactly the same results. For the
>> affy package see
>>
>> http://bmbolstad.com/misc/MAS5diff/Mas5difference.html
>>
>> for an explanation of the differences.
>>
>> Best,
>>
>> Jim
>>
>>
> Thanks for the reply. It looks pretty close.
>
> So is the expresso() command listed on the page
> *
> eset <- expresso(Data,
> bgcorrect.method="mas",normalize=FALSE,pmcorrect.method="mas",summary.method="mas")
> *
>
> be the same as the justMAS()?
>
> Thanks in advance.
>
> Timothy
>
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