[BioC] MAS5 and GCOC difference to get CEL files

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Mon Sep 13 19:24:18 CEST 2004

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

I wish Affymetrix had a consistent way of naming things : GeneChip
software, MAS 4.0, MAS 5.0, GCOS.

I suppose it is no different than Windows 3.1, Windows 95, Windows NT,
Windows 98, Window ME, Window 2000, Windows XP

On Mon, 2004-09-13 at 14:23, James W. MacDonald wrote:
> Adaikalavan Ramasamy wrote:
> > I assume that you used 
> >  i)  12 CEL files to obtain MAS 5.0 via R and
> >  ii) 4 CEL files via GCOS (GeneSpring Operating Software ?) which I
> > assume also gives MAS 5.0
> GCOS stands for GeneChip Operating Software, and is the Affymetrix 
> replacement for MAS5.
> > On Mon, 2004-09-13 at 10:41, Delphine Fleury wrote:
> > 
> >>Dear all,
> >>I am analyzing affymetrix data ATH1 from the same biological experiment 
> >>(material growth, harvesting and RNA extraction done at the same time in 
> >>the same conditions) but hybridized at 2 different dates (the 2d set 
> >>done 1 year later). So , 12 chips were preprocessed with MAS5 getting 
> >>CEL files and 4 chips with GCOS.
> >>At first, I see that the size of the CEL files are about 11 MB for the 
> >>12 chips and about 5 MB for the 4 last chips. 
> The 12 files are in the old-style text format, whereas the 4 newer files 
> are in binary format, and hence are smaller.
> Secondly, the mean signal
> >>of the 4 last chips is lower than those from the 12 chips (cf boxplots 
> >>before normalization, and AffyPLM). 
> >>Is it possible that the lower signal is related to the preprocessing 
> >>method from GCOS ?
> Possible, but not likely. You should check with whoever did the 
> processing and see if they used the ENZO kit or the new IVT kit from 
> Affy with the last four chips. I am betting that they switched to the 
> new IVT kit. If so, this is probably very bad news, because I don't 
> think the results will be comparable. I know for a fact that RMA, GCRMA, 
> and MAS5 will not give comparable results for the two IVT protocols. For 
> the next month or two you can still get the ENZO kit, so if you need 
> data from the other four chips I would recommend re-doing them with the 
> ENZO kit.
> >>Is there someone who observe the same things ?
> >>Could it be a problem to analyse all chips together ?
> >>Thanks
> >>Delphine
> >>
> > 
> > 
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