simpleaffy problem
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@ariel-chernomoretz-885
Last seen 7.2 years ago
Hi, I am trying to reproduce the simpleaffy vignette examples and found some weird behavior: I read the cel files > setwd("GQ002/tissu_06/CEL") > x<-read.affy("covdesc") > pData(x) sample treatment GQ002F01D06C4R1.CEL 1 n GQ002F01D06C4R2.CEL 2 n GQ002F01D06C4R3.CEL 3 n GQ002F02D06C4R1.CEL 4 g GQ002F02D06C4R2.CEL 5 g GQ002F02D06C4R3.CEL 6 g I get the following when apply mas5 processing method > x.mas<-call.exprs(x,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ......done. scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F01D06C4R2.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F01D06C4R3.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R1.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R2.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R3.CEL 8.97428766057367e-15 and the following error message while trying to perform a pairwise comparation: > results<-pairwise.comparison(x.mas,"treatment",spots=x) Getting probe level data... Computing p-values Doing PMA Calls Error in get.fold.change.and.t.test(x, group, members, logged = logged, : NA/NaN/Inf in foreign function call (arg 1) Moreover if I read again the same CEL files and repeat the mas5.0 calculation I get the following new scale factors: > xx<-read.affy("covdesc") > xx.mas<-call.exprs(xx,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ......done. scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL 6.52404421935092e-34 Scale factor for: ./GQ002F01D06C4R2.CEL 29644.0460038727 Scale factor for: ./GQ002F01D06C4R3.CEL 8.45337767106362e-171 Scale factor for: ./GQ002F02D06C4R1.CEL 28417.5423558275 Scale factor for: ./GQ002F02D06C4R2.CEL 8.45337767106362e-171 Scale factor for: ./GQ002F02D06C4R3.CEL 8.45337767106362e-171 Is there a problem reading the cel files? R is not started in the CEL files directory, is that a problem? I am running R 1.9.0 on Mac OS X 10.3.5 affy 1.4.30 simpleaffy 1.2.1 Any help would be apreciated Ariel./ Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339
probe simpleaffy probe simpleaffy • 736 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.2 years ago
Hi Ariel, Sorry for taking a few days to reply. I guess the simple answer is that I don't know, however, I've not had access to a Mac to test simpleaffy on: http://bioinformatics.picr.man.ac.uk/simpleaffy/index.jsp my instinct is that this is where the problem lies - the scale factors look very odd, and there's a fair amount of C-code interfacing with R under the bonnet. I'll try to look into things and let you know what I find. In the meantime try: x.mas<-call.exprs(x,"mas5-R"), which uses the R implementation in expresso instead... As I said, I've not done any testing on macs so be careful! :-) Good luck, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Ariel Chernomoretz Sent: 18 August 2004 20:20 To: bioconductor@stat.math.ethz.ch Subject: [BioC] simpleaffy problem Hi, I am trying to reproduce the simpleaffy vignette examples and found some weird behavior: I read the cel files > setwd("GQ002/tissu_06/CEL") > x<-read.affy("covdesc") > pData(x) sample treatment GQ002F01D06C4R1.CEL 1 n GQ002F01D06C4R2.CEL 2 n GQ002F01D06C4R3.CEL 3 n GQ002F02D06C4R1.CEL 4 g GQ002F02D06C4R2.CEL 5 g GQ002F02D06C4R3.CEL 6 g I get the following when apply mas5 processing method > x.mas<-call.exprs(x,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ......done. scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F01D06C4R2.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F01D06C4R3.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R1.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R2.CEL 8.97428766057367e-15 Scale factor for: ./GQ002F02D06C4R3.CEL 8.97428766057367e-15 and the following error message while trying to perform a pairwise comparation: > results<-pairwise.comparison(x.mas,"treatment",spots=x) Getting probe level data... Computing p-values Doing PMA Calls Error in get.fold.change.and.t.test(x, group, members, logged = logged, : NA/NaN/Inf in foreign function call (arg 1) Moreover if I read again the same CEL files and repeat the mas5.0 calculation I get the following new scale factors: > xx<-read.affy("covdesc") > xx.mas<-call.exprs(xx,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ......done. scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL 6.52404421935092e-34 Scale factor for: ./GQ002F01D06C4R2.CEL 29644.0460038727 Scale factor for: ./GQ002F01D06C4R3.CEL 8.45337767106362e-171 Scale factor for: ./GQ002F02D06C4R1.CEL 28417.5423558275 Scale factor for: ./GQ002F02D06C4R2.CEL 8.45337767106362e-171 Scale factor for: ./GQ002F02D06C4R3.CEL 8.45337767106362e-171 Is there a problem reading the cel files? R is not started in the CEL files directory, is that a problem? I am running R 1.9.0 on Mac OS X 10.3.5 affy 1.4.30 simpleaffy 1.2.1 Any help would be apreciated Ariel./ Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Hi Crispin, I tried running the expresso implementation as you suggested but again I get the same error when applying 'pairwise.comparison' I tried also with different processing method but with no luck. Thanks for your attention Ariel,. > setwd("GQ002/tissu_06/CEL") > x<-read.affy("covdesc") > x.mas<-call.exprs(x,"mas5-R") background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 12488 ids to be processed | | |####################| > results<-pairwise.comparison(x.mas,"treatment",spots=x) Getting probe level data... Computing p-values Doing PMA Calls Error in pairwise.comparison(x.mas, "treatment", spots = x) : couldn't find function "calls<-" > On 23 ao?t 2004, at 07:36, Crispin Miller wrote: > Hi Ariel, > Sorry for taking a few days to reply. I guess the simple answer is that > I don't know, however, I've not had access to a Mac to test simpleaffy > on: > > http://bioinformatics.picr.man.ac.uk/simpleaffy/index.jsp > > my instinct is that this is where the problem lies - the scale factors > look very odd, and there's a fair amount of C-code interfacing with R > under the bonnet. I'll try to look into things and let you know what I > find. In the meantime try: > > x.mas<-call.exprs(x,"mas5-R"), which uses the R implementation in > expresso instead... > > As I said, I've not done any testing on macs so be careful! :-) > Good luck, > > Crispin > > > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Ariel > Chernomoretz > Sent: 18 August 2004 20:20 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] simpleaffy problem > > Hi, > I am trying to reproduce the simpleaffy vignette examples and found > some > weird behavior: > I read the cel files >> setwd("GQ002/tissu_06/CEL") >> x<-read.affy("covdesc") >> pData(x) > sample treatment > GQ002F01D06C4R1.CEL 1 n > GQ002F01D06C4R2.CEL 2 n > GQ002F01D06C4R3.CEL 3 n > GQ002F02D06C4R1.CEL 4 g > GQ002F02D06C4R2.CEL 5 g > GQ002F02D06C4R3.CEL 6 g > > I get the following when apply mas5 processing method >> x.mas<-call.exprs(x,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ......done. > scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL > 8.97428766057367e-15 > Scale factor for: ./GQ002F01D06C4R2.CEL 8.97428766057367e-15 > Scale factor for: ./GQ002F01D06C4R3.CEL 8.97428766057367e-15 > Scale factor for: ./GQ002F02D06C4R1.CEL 8.97428766057367e-15 > Scale factor for: ./GQ002F02D06C4R2.CEL 8.97428766057367e-15 > Scale factor for: ./GQ002F02D06C4R3.CEL 8.97428766057367e-15 > > and the following error message while trying to perform a pairwise > comparation: >> results<-pairwise.comparison(x.mas,"treatment",spots=x) > Getting probe level data... > Computing p-values > Doing PMA Calls > Error in get.fold.change.and.t.test(x, group, members, logged = logged, > : > NA/NaN/Inf in foreign function call (arg 1) > > Moreover if I read again the same CEL files and repeat the mas5.0 > calculation I get the following new scale factors: >> xx<-read.affy("covdesc") >> xx.mas<-call.exprs(xx,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ......done. > scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL > 6.52404421935092e-34 > Scale factor for: ./GQ002F01D06C4R2.CEL 29644.0460038727 > Scale factor for: ./GQ002F01D06C4R3.CEL 8.45337767106362e-171 > Scale factor for: ./GQ002F02D06C4R1.CEL 28417.5423558275 > Scale factor for: ./GQ002F02D06C4R2.CEL 8.45337767106362e-171 > Scale factor for: ./GQ002F02D06C4R3.CEL 8.45337767106362e-171 > > Is there a problem reading the cel files? R is not started in the CEL > files directory, is that a problem? > > I am running R 1.9.0 on Mac OS X 10.3.5 > affy 1.4.30 > simpleaffy 1.2.1 > > Any help would be apreciated > Ariel./ > > Ariel Chernomoretz, Ph.D. > Centre de recherche du CHUL > 2705 Blv Laurier, bloc T-367 > Sainte-Foy, Qc > G1V 4G2 > (418)-525-4444 ext 46339 > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use of the > person(s) ('the intended recipient') to whom it was addressed. Any > views or opinions presented are solely those of the author and do not > necessarily represent those of the Paterson Institute for Cancer > Research or the Christie Hospital NHS Trust. It may contain > information that is privileged & confidential within the meaning of > applicable law. Accordingly any dissemination, distribution, copying, > or other use of this message, or any of its contents, by any person > other than the intended recipient may constitute a breach of civil or > criminal law and is strictly prohibited. If you are NOT the intended > recipient please contact the sender and dispose of this e-mail as soon > as possible. > > Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339
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