[BioC] MAS 5.0
Wilkinson, Mark
Mark.Wilkinson@stjude.org
Wed, 22 Jan 2003 12:58:00 -0600
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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