[BioC] MAS 5.0
Benjamin Milo BOLSTAD
bolstad@stat.berkeley.edu
Wed, 22 Jan 2003 11:29:04 -0800 (PST)
The MAS 5.0 implementation is based upon availiable documentation.
Clearly it might be impossible to completely duplicate Affymetrix, since
there are pieces of their documentation that are left a little vague.
Ben
On Wed, 22 Jan 2003, Wilkinson, Mark wrote:
>
> This issue in general has kept me somewhat reluctant to use the affy
> package.
>
> To the affy package authors: is the idea for affy to reproduce the
> functionality of MAS 5.0 (at least for some parts)? In other words, should
> I be able to do probe level summaries exactly like MAS5, or is affy's
> version just a close approximation?
>
>
>
> Mark Wilkinson
> Informatics Analyst
> St. Jude Children's Research Hospital
> Department of Pharmaceutical Sciences
>
> The opinions expressed here are my own and do not necessarily represent
> those of St. Jude Children's Research Hospital.
>
>
> -----Original Message-----
> From: Helene Boucher [mailto:bouhel01@borabora.crchul.ulaval.ca]
> Sent: Wednesday, January 22, 2003 10:09 AM
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] MAS 5.0
>
>
>
> I tried expresso to reproduce expression measures from MAS 5.0 but I get a
> slight
> difference from Affymetrix as illustrated on a set of 3 chips for selected
> probe
> sets. Any idea why that is? The version of Unix we have is SunOS Release
> 5.8.
>
> Thanks,
>
> Helene
>
>
> 100001_at 29.6222834908728 10.2880336221679
> 80.7973366171763
> 100002_at 9.94107964466495 62.9653009129815
> 53.7356175596969
> 100003_at 2262.85860839992 1539.08193903367
> 1910.0212276237
> 100004_at 305.100816246875 188.181043441888
> 239.902666074234
> 100005_at 434.482366404616 638.860562906946
> 589.86003783735
> 100006_at 61.9587790672468 32.9005081415387
> 61.5914892307955
> 100007_at 890.772109484179 988.46987085589 1076.17589775836
> 100009_r_at 89.4108950323307 46.1650654835421
> 54.0252748779586
> 100010_at 227.251880233698 401.164278682326
> 424.746403324436
> 100011_at 1157.66237359318 702.613181714498
> 882.033123210299
> 100012_at 893.256638440421 1511.96440725101
> 2054.18415149103
> ----------------------------------------------------------------------------
> --------
>
>
> 100001_at 16 16 26.0 A 0.781017
>
>
>
> 100002_at 16 16 10.2 A 0.910595
>
>
>
> 100003_at 16 16 2271.8 P 0.000219
>
>
>
> 100004_at 16 16 302.2 P 0.004863
>
>
>
> 100005_at 16 16 439.1 P 0.006532
>
>
>
> 100006_at 16 16 63.5 A 0.358690
>
>
>
> 100007_at 16 16 894.7 P 0.001354
>
>
>
> 100009_r_at 16 16 90.2 P 0.000805
>
>
>
> 100010_at 16 16 227.4 P 0.009985
> ----------------------------------------------------------------------------
> ---------
> 100001_at 16 16 11.0 A 0.602006
>
>
>
> 100002_at 16 16 58.8 A 0.438361
>
>
>
> 100003_at 16 16 1545.5 P 0.000219
>
>
>
> 100004_at 16 16 191.7 P 0.011447
>
>
>
> 100005_at 16 16 641.4 P 0.002617
>
>
>
> 100006_at 16 16 33.7 A 0.117160
>
>
>
> 100007_at 16 16 992.9 P 0.001141
>
>
>
> 100009_r_at 16 16 47.4 P 0.011447
>
>
>
> 100010_at 16 16 402.6 P 0.001354
> ----------------------------------------------------------------------------
> ---------
> 100001_at 16 16 81.1 A 0.438361
>
>
>
> 100002_at 16 16 44.4 A 0.581931
>
>
>
> 100003_at 16 16 1917.2 P 0.000219
>
>
>
> 100004_at 16 16 244.2 P 0.031336
>
>
>
> 100005_at 16 16 591.0 P 0.001354
>
>
>
> 100006_at 16 16 62.9 A 0.089405
>
>
>
> 100007_at 16 16 1080.6 P 0.000673
>
>
>
> 100009_r_at 16 16 54.5 P 0.011447
>
>
>
> 100010_at 16 16 428.1 P 0.000959
> ----------------------------------------------------------------------------
> --------
>
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