[BioC] MAS5 and GCOC difference to get CEL files
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 ?
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