[BioC] MAS5 and GCOC difference to get CEL files

Matthew Hannah Hannah at mpimp-golm.mpg.de
Wed Sep 15 09:35:22 CEST 2004


The Affymetrix software GCOS 1.0 currently uses MAS5, but will (when
they get round to it) use the PLIER algorithm (which is more like RMA
style exprs measures). As I understand when this happens the software
will be split - GCOS 2.0 will operate the system and produce the .DAT
and .CEL files. GREX will do the data analysis - PLIER +/- mm
correction, MAS5, ANOVA, clustering, Venn diagrams.....

As for when - no idea, last december we were told beta testing will
finish in Q1 of this year.... but I guess they were more than abit
optimistic. Sorry for those people who spent $10-20k? for a years use of
an outdated and repackaged MAS5....

In addition to the binary .CEL files, GCOS also uses a different
gridding algorithm, but I understand it shouldn't lead to differences.
As for differences on chips run a year apart, RNA extraction, quality,
labelling, person doing it could all affect things. Also check that your
service provider hasn't changed their scanner or settings? If you ran
test chips, look at our suggestion last month to do AffyPLM on the test
chips to identify labelling differences.

https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-August/005800.
html

Cheers,
Matt



On Sep 13, 2004, at 7:24 PM, Adaikalavan Ramasamy wrote:

> Thanks. So GCOS is also an algorithm for producing expression
measures.

GCOS should be: 'Gene Chip Operating System',

it is an environment in which you have all the software provided by
Affymetrix in order to:

- manage scanner, fluidic station etc.
- manage, organize and storage all the experiments in a database
- analyze your chip with MAS5 algorithm
- made just a very little bit of data-mining...

> I quickly skimmed through the GCOS User Guide manual but did not find
> the details of the algorithm. Could someone be kind enough to tell me
> where I can find the algorithm and how it is different from MAS 5.0.

GCOS use MAS5 algorithm...

http://www.affymetrix.com/Auth/support/downloads/manuals/ 
expression_s1_manual.pdf
http://www.affymetrix.com/Auth/support/downloads/manuals/ 
data_analysis_fundamentals_manual.pdf


HTH

Remo



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