simpleaffy and yeast2cdf problems
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Dan Swan ▴ 50
@dan-swan-1869
Last seen 7.3 years ago
Hi Bioconductorites, I've seen references to this problem in 2005 (https://stat.ethz.ch/pipermail/bioconductor/2005-November/010865.html ) and 2006 (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012480.html), the former suggesting it should be fixed, but I'm still having the same issue. I just want some quick and dirty QC measures on some chips I am pretty sure are duff. following along with the outline in the "QC and Affymetrix data" pdf: > ampli.data<-read.affy("phenodata") > ampli.eset<-call.exprs(ampli.data,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ..............................done. scaling to a TGT of 100 ... Scale factor for: Yeast0wt1.CEL 0.1877573661054 Scale factor for: Yeast0wt2.CEL 0.169107349891647 Scale factor for: Yeast0wt3.CEL 0.176890842235261 Scale factor for: Yeast1wt1.CEL 0.114515875199183 Scale factor for: Yeast1wt2.CEL 0.132867931840117 Scale factor for: Yeast1wt3.CEL 0.201211860669323 Scale factor for: Yeast2wt1.CEL 0.120553407334518 Scale factor for: Yeast2wt2.CEL 0.110981821370179 Scale factor for: Yeast2wt3.CEL 0.12635084302873 Scale factor for: Yeast3wt1.CEL 0.133156738139789 Scale factor for: Yeast3wt2.CEL 0.119446187371786 Scale factor for: Yeast3wt3.CEL 0.136591273338234 Scale factor for: Yeast4wt1.CEL 0.143174910484902 Scale factor for: Yeast4wt2.CEL 0.127534874666620 Scale factor for: Yeast4wt3.CEL 0.177048335355844 Scale factor for: Yeast0mut1.CEL 0.126568563373901 Scale factor for: Yeast0mut2.CEL 0.177828594244113 Scale factor for: Yeast0mut3.CEL 0.113037148372224 Scale factor for: Yeast1mut1.CEL 0.125912932405511 Scale factor for: Yeast1mut2.CEL 0.167309068269027 Scale factor for: Yeast1mut3.CEL 0.134897445983855 Scale factor for: Yeast2mut1.CEL 0.136284006808245 Scale factor for: Yeast2mut2.CEL 0.197169068283275 Scale factor for: Yeast2mut3.CEL 0.149844757694802 Scale factor for: Yeast3mut1.CEL 0.119095781239726 Scale factor for: Yeast3mut2.CEL 0.155941398564195 Scale factor for: Yeast3mut3.CEL 0.144702217239922 Scale factor for: Yeast4mut1.CEL 0.183634382620250 Scale factor for: Yeast4mut2.CEL 0.180182357563251 Scale factor for: Yeast4mut3.CEL 0.152303319246271 > qc.data<-qc(ampli.data, ampli.eset) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf which is the same error that has been reported before. sessionInfo() follows: > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" [8] "methods" "base" other attached packages: yeast2cdf simpleaffy genefilter survival affy affyio Biobase "1.14.0" "2.8.0" "1.12.0" "2.30" "1.12.2" "1.2.0" "1.12.2" any help would be appreciated. regards, Dan -- Research Support Officer, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech: Rooms M.2046/M.2046A - Mon/Wed) Tel: +44 (0)191 246 4833 (Devonshire: Rooms G.25/G.26 - Thu/Fri) Website: http://bsu.ncl.ac.uk/
Survival cdf genefilter affy simpleaffy Survival cdf genefilter affy simpleaffy • 850 views
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.3 years ago
Hi Dan, See the very recent post by Greg Alford: https://stat.ethz.ch/pipermail/bioconductor/2007-January/015514.html They have modified the code of qc() so that it will work for unknown chip types. Although he is calling his code soybean.mod.qc.affy(), there is nothing specific for the soybean array so it can be used for any chip type. However, it doesn't give all the information that qc() does; the spike-in probes, other qc probes and bioB hyb controls are specific for each chip and had to be left out. If you know these for your chip type, you might be able to modify the original code (commented out in soybean.mod.qc.affy) to include them. Cheers, Jenny At 05:49 AM 1/8/2007, Dan Swan wrote: >Hi Bioconductorites, > >I've seen references to this problem in 2005 >(https://stat.ethz.ch/pipermail/bioconductor/2005-November/010865.htm l) >and 2006 (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012480.html), >the former suggesting it should be fixed, but I'm still having the >same issue. > >I just want some quick and dirty QC measures on some chips I am pretty >sure are duff. > >following along with the outline in the "QC and Affymetrix data" pdf: > > > ampli.data<-read.affy("phenodata") > > ampli.eset<-call.exprs(ampli.data,"mas5") >Background correcting >Retrieving data from AffyBatch...done. >Computing expression calls... >..............................done. >scaling to a TGT of 100 ... >Scale factor for: Yeast0wt1.CEL 0.1877573661054 >Scale factor for: Yeast0wt2.CEL 0.169107349891647 >Scale factor for: Yeast0wt3.CEL 0.176890842235261 >Scale factor for: Yeast1wt1.CEL 0.114515875199183 >Scale factor for: Yeast1wt2.CEL 0.132867931840117 >Scale factor for: Yeast1wt3.CEL 0.201211860669323 >Scale factor for: Yeast2wt1.CEL 0.120553407334518 >Scale factor for: Yeast2wt2.CEL 0.110981821370179 >Scale factor for: Yeast2wt3.CEL 0.12635084302873 >Scale factor for: Yeast3wt1.CEL 0.133156738139789 >Scale factor for: Yeast3wt2.CEL 0.119446187371786 >Scale factor for: Yeast3wt3.CEL 0.136591273338234 >Scale factor for: Yeast4wt1.CEL 0.143174910484902 >Scale factor for: Yeast4wt2.CEL 0.127534874666620 >Scale factor for: Yeast4wt3.CEL 0.177048335355844 >Scale factor for: Yeast0mut1.CEL 0.126568563373901 >Scale factor for: Yeast0mut2.CEL 0.177828594244113 >Scale factor for: Yeast0mut3.CEL 0.113037148372224 >Scale factor for: Yeast1mut1.CEL 0.125912932405511 >Scale factor for: Yeast1mut2.CEL 0.167309068269027 >Scale factor for: Yeast1mut3.CEL 0.134897445983855 >Scale factor for: Yeast2mut1.CEL 0.136284006808245 >Scale factor for: Yeast2mut2.CEL 0.197169068283275 >Scale factor for: Yeast2mut3.CEL 0.149844757694802 >Scale factor for: Yeast3mut1.CEL 0.119095781239726 >Scale factor for: Yeast3mut2.CEL 0.155941398564195 >Scale factor for: Yeast3mut3.CEL 0.144702217239922 >Scale factor for: Yeast4mut1.CEL 0.183634382620250 >Scale factor for: Yeast4mut2.CEL 0.180182357563251 >Scale factor for: Yeast4mut3.CEL 0.152303319246271 > > qc.data<-qc(ampli.data, ampli.eset) >Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about >chip type: yeast2cdf > >which is the same error that has been reported before. > >sessionInfo() follows: > > > sessionInfo() >R version 2.4.1 (2006-12-18) >i386-pc-mingw32 > >locale: >LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >Kingdom.1252;LC_MONETARY=English_United >Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > >attached base packages: >[1] "splines" "tools" "stats" "graphics" "grDevices" >"utils" "datasets" >[8] "methods" "base" > >other attached packages: > yeast2cdf simpleaffy genefilter survival affy affyio Biobase > "1.14.0" "2.8.0" "1.12.0" "2.30" "1.12.2" "1.2.0" "1.12.2" > >any help would be appreciated. > >regards, > >Dan > >-- >Research Support Officer, Bioinformatics Support Unit, >Institute for Cell and Molecular Biosciences, >Faculty of Medical Sciences, Framlington Place, >University of Newcastle upon Tyne, Newcastle, NE2 4HH >Tel: +44 (0)191 222 7253 (Leech: Rooms M.2046/M.2046A - Mon/Wed) >Tel: +44 (0)191 246 4833 (Devonshire: Rooms G.25/G.26 - Thu/Fri) >Website: http://bsu.ncl.ac.uk/ > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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@alvord-greg-dms-contr-1603
Last seen 7.3 years ago
Hi Dan - This is the post I sent out only last week that may assist you with your problem. https://stat.ethz.ch/pipermail/bioconductor/2007-January/015514.html We ran into a similar problem with the soybeancdf environment. Hope this helps. Greg -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dan Swan Sent: Monday, January 08, 2007 6:49 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] simpleaffy and yeast2cdf problems Hi Bioconductorites, I've seen references to this problem in 2005 (https://stat.ethz.ch/pipermail/bioconductor/2005-November/010865.html ) and 2006 (https://stat.ethz.ch/pipermail/bioconductor/2006-March/012480.html), the former suggesting it should be fixed, but I'm still having the same issue. I just want some quick and dirty QC measures on some chips I am pretty sure are duff. following along with the outline in the "QC and Affymetrix data" pdf: > ampli.data<-read.affy("phenodata") > ampli.eset<-call.exprs(ampli.data,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ..............................done. scaling to a TGT of 100 ... Scale factor for: Yeast0wt1.CEL 0.1877573661054 Scale factor for: Yeast0wt2.CEL 0.169107349891647 Scale factor for: Yeast0wt3.CEL 0.176890842235261 Scale factor for: Yeast1wt1.CEL 0.114515875199183 Scale factor for: Yeast1wt2.CEL 0.132867931840117 Scale factor for: Yeast1wt3.CEL 0.201211860669323 Scale factor for: Yeast2wt1.CEL 0.120553407334518 Scale factor for: Yeast2wt2.CEL 0.110981821370179 Scale factor for: Yeast2wt3.CEL 0.12635084302873 Scale factor for: Yeast3wt1.CEL 0.133156738139789 Scale factor for: Yeast3wt2.CEL 0.119446187371786 Scale factor for: Yeast3wt3.CEL 0.136591273338234 Scale factor for: Yeast4wt1.CEL 0.143174910484902 Scale factor for: Yeast4wt2.CEL 0.127534874666620 Scale factor for: Yeast4wt3.CEL 0.177048335355844 Scale factor for: Yeast0mut1.CEL 0.126568563373901 Scale factor for: Yeast0mut2.CEL 0.177828594244113 Scale factor for: Yeast0mut3.CEL 0.113037148372224 Scale factor for: Yeast1mut1.CEL 0.125912932405511 Scale factor for: Yeast1mut2.CEL 0.167309068269027 Scale factor for: Yeast1mut3.CEL 0.134897445983855 Scale factor for: Yeast2mut1.CEL 0.136284006808245 Scale factor for: Yeast2mut2.CEL 0.197169068283275 Scale factor for: Yeast2mut3.CEL 0.149844757694802 Scale factor for: Yeast3mut1.CEL 0.119095781239726 Scale factor for: Yeast3mut2.CEL 0.155941398564195 Scale factor for: Yeast3mut3.CEL 0.144702217239922 Scale factor for: Yeast4mut1.CEL 0.183634382620250 Scale factor for: Yeast4mut2.CEL 0.180182357563251 Scale factor for: Yeast4mut3.CEL 0.152303319246271 > qc.data<-qc(ampli.data, ampli.eset) Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: yeast2cdf which is the same error that has been reported before. sessionInfo() follows: > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" [8] "methods" "base" other attached packages: yeast2cdf simpleaffy genefilter survival affy affyio Biobase "1.14.0" "2.8.0" "1.12.0" "2.30" "1.12.2" "1.2.0" "1.12.2" any help would be appreciated. regards, Dan -- Research Support Officer, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech: Rooms M.2046/M.2046A - Mon/Wed) Tel: +44 (0)191 246 4833 (Devonshire: Rooms G.25/G.26 - Thu/Fri) Website: http://bsu.ncl.ac.uk/ _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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