MAS5 and GCOC difference to get CEL files
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@delphine-fleury-414
Last seen 10.2 years ago
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. 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 ? Is there someone who observe the same things ? Could it be a problem to analyse all chips together ? Thanks Delphine -- ================================================================== Delphine Fleury DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:defle@psb.ugent.be http://www.psb.ugent.be
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@adaikalavan-ramasamy-675
Last seen 10.2 years ago
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 IMHO, you cannot compare these 12 expression measures to the 4 files. It would be interesting to compare the MAS 5.0 expression from the combined 16 CEL files via R and GCOS. This would tell you to which extent the softwares differ but this page could be of help http://stat- www.berkeley.edu/users/bolstad/MAS5diff/Mas5difference.html Personally, I would not combine any expression measure performed with two different softwares because any significant differences could be either real or simply due to software differences. As for the differing file sizes, could it be due to the new GCOS binary format. I not familiar with GCOS at all. Regards, Adai 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. 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 ? > Is there someone who observe the same things ? > Could it be a problem to analyse all chips together ? > Thanks > Delphine >
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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 >> > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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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 > >> > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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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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@matthew-hannah-621
Last seen 10.2 years ago
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/00580 0. 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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