expresso error
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@anjan-purkayastha-4273
Last seen 9.6 years ago
Hi, I have created an affybatch object from 3 cel files. The files have data from Affymetrix's Mouse Expression (Oligonucleotide) array. Affybatch object was created by command: testAffy <- ReadAffy() In the next step I tried to use expresso to adjust background using RMA and normalize using loess, using the command: testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", normalize.method= "loess") Here is the output: background correction: rma normalization: loess PM/MM correction : expression values: background correcting...done. normalizing...Done with 1 vs 2 in iteration 1 Done with 1 vs 3 in iteration 1 Done with 2 vs 3 in iteration 1 1 0.0176947 done. Error in function (classes, fdef, mtable) : unable to find an inherited method for function "computeExprSet", for signature "AffyBatch", "NULL", "NULL" The testAffy.loess object was not created. Any idea why I am getting an error on running the expresso command? Thanks in advance. Anjan -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 16 days ago
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please provide your sessionInfo() and the specific class of array in use -- there are various mouse expression arrays from affy. On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Hi, > I have created an affybatch object from 3 cel files. The files have data > from Affymetrix's Mouse Expression (Oligonucleotide) array. > Affybatch object was created by command: > testAffy <- ReadAffy() > > In the next step I tried to use expresso to adjust background using RMA and > normalize using loess, using the command: > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", > normalize.method= "loess") > Here is the output: > background correction: rma > normalization: loess > PM/MM correction : > expression values: > background correcting...done. > normalizing...Done with 1 vs 2 in iteration 1 > Done with 1 vs 3 in iteration 1 > Done with 2 vs 3 in iteration 1 > 1 0.0176947 > done. > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "computeExprSet", for > signature "AffyBatch", "NULL", "NULL" > > The testAffy.loess object was not created. ?Any idea why I am getting an > error on running the expresso command? > Thanks in advance. > Anjan > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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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Hi Vincent, I used the Mouse Genome 430 2.0 Array ( http://www.affymetrix.com/support/technical/byproduct.affx?product=moe 430-20 ) Here is my session info: R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0 gcrma_2.20.0 genefilter_1.30.0 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 Biostrings_2.16.9 DBI_0.2-5 IRanges_1.6.17 preprocessCore_1.10.0 [8] RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 xtable_1.5-6 Thanks in advance for your help. Anjan On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > please provide your sessionInfo() and the specific class of array in > use -- there are various mouse > expression arrays from affy. > > On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA > <anjan.purkayastha@gmail.com> wrote: > > Hi, > > I have created an affybatch object from 3 cel files. The files have data > > from Affymetrix's Mouse Expression (Oligonucleotide) array. > > Affybatch object was created by command: > > testAffy <- ReadAffy() > > > > In the next step I tried to use expresso to adjust background using RMA > and > > normalize using loess, using the command: > > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", > > normalize.method= "loess") > > Here is the output: > > background correction: rma > > normalization: loess > > PM/MM correction : > > expression values: > > background correcting...done. > > normalizing...Done with 1 vs 2 in iteration 1 > > Done with 1 vs 3 in iteration 1 > > Done with 2 vs 3 in iteration 1 > > 1 0.0176947 > > done. > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "computeExprSet", for > > signature "AffyBatch", "NULL", "NULL" > > > > The testAffy.loess object was not created. Any idea why I am getting an > > error on running the expresso command? > > Thanks in advance. > > Anjan > > > > -- > > =================================== > > anjan purkayastha, phd. > > research associate > > fas center for systems biology, > > harvard university > > 52 oxford street > > cambridge ma 02138 > > phone-703.740.6939 > > =================================== > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]
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I reproduced your experience. The problem is that the software lets you get away with not specifying the summary.method and the pmcorrect.method at the interface, but when it gets around to doing the expression computations, if it gets NULLs (the default) it dies. expresso() should probably force the user to put something in or put reasonable defaults. if you add summary.method = "avgdiff" and pmcorrect.method="pmonly" to your call, for example, it will complete. you have to look over the options for those methods; the doc is not crystal clear in all places. for some parameters function calls will tell you the options available > bgcorrect.methods() [1] "bg.correct" "mas" "none" "rma" > pmcorrect.methods() [1] "mas" "methods" "pmonly" "subtractmm" summary.methods() does not seem to exist. but > generateExprSet.methods() [1] "avgdiff" "liwong" "mas" "medianpolish" "playerout" seems to supply the relevant options for that parameter. On Wed, Oct 6, 2010 at 9:59 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Hi Vincent, > I used the Mouse Genome 430 2.0 Array > (http://www.affymetrix.com/support/technical/byproduct.affx?product= moe430-20) > > Here is my session info: > R version 2.11.1 (2010-05-31) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > other attached packages: > [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0? gcrma_2.20.0 > genefilter_1.30.0? affy_1.26.1??????? Biobase_2.8.0 > > loaded via a namespace (and not attached): > ?[1] affyio_1.16.0???????? annotate_1.26.1?????? AnnotationDbi_1.10.2 > Biostrings_2.16.9???? DBI_0.2-5???????????? IRanges_1.6.17 > preprocessCore_1.10.0 > ?[8] RSQLite_0.9-2???????? splines_2.11.1??????? survival_2.35-8 > tools_2.11.1????????? xtable_1.5-6 > > Thanks in advance for your help. > Anjan > > > On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> > wrote: >> >> please provide your sessionInfo() and the specific class of array in >> use -- there are various mouse >> expression arrays from affy. >> >> On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA >> <anjan.purkayastha at="" gmail.com=""> wrote: >> > Hi, >> > I have created an affybatch object from 3 cel files. The files have data >> > from Affymetrix's Mouse Expression (Oligonucleotide) array. >> > Affybatch object was created by command: >> > testAffy <- ReadAffy() >> > >> > In the next step I tried to use expresso to adjust background using RMA >> > and >> > normalize using loess, using the command: >> > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", >> > normalize.method= "loess") >> > Here is the output: >> > background correction: rma >> > normalization: loess >> > PM/MM correction : >> > expression values: >> > background correcting...done. >> > normalizing...Done with 1 vs 2 in iteration 1 >> > Done with 1 vs 3 in iteration 1 >> > Done with 2 vs 3 in iteration 1 >> > 1 0.0176947 >> > done. >> > Error in function (classes, fdef, mtable) ?: >> > ?unable to find an inherited method for function "computeExprSet", for >> > signature "AffyBatch", "NULL", "NULL" >> > >> > The testAffy.loess object was not created. ?Any idea why I am getting an >> > error on running the expresso command? >> > Thanks in advance. >> > Anjan >> > >> > -- >> > =================================== >> > anjan purkayastha, phd. >> > research associate >> > fas center for systems biology, >> > harvard university >> > 52 oxford street >> > cambridge ma 02138 >> > phone-703.740.6939 >> > =================================== >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > > > > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== >
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Vince, Thanks. So it looks like there is no way for me to use expresso to perform background correction, normalization and then examine the data before proceeding to other downstream analyses. Any suggestions on how I can accomplish this without the help of expresso? Thanks, Anjan On Wed, Oct 6, 2010 at 10:32 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > I reproduced your experience. The problem is that the software lets > you get away > with not specifying the summary.method and the pmcorrect.method at the > interface, but > when it gets around to doing the expression computations, if it gets > NULLs (the default) > it dies. expresso() should probably force the user to put something > in or put reasonable > defaults. > > if you add summary.method = "avgdiff" and pmcorrect.method="pmonly" to > your call, for example, > it will complete. you have to look over the options for those > methods; the doc is not crystal > clear in all places. for some parameters function calls will tell you > the options available > > > bgcorrect.methods() > [1] "bg.correct" "mas" "none" "rma" > > pmcorrect.methods() > [1] "mas" "methods" "pmonly" "subtractmm" > > summary.methods() does not seem to exist. but > > > generateExprSet.methods() > [1] "avgdiff" "liwong" "mas" "medianpolish" "playerout" > > seems to supply the relevant options for that parameter. > > > On Wed, Oct 6, 2010 at 9:59 PM, ANJAN PURKAYASTHA > <anjan.purkayastha@gmail.com> wrote: > > Hi Vincent, > > I used the Mouse Genome 430 2.0 Array > > ( > http://www.affymetrix.com/support/technical/byproduct.affx?product=m oe430-20 > ) > > > > Here is my session info: > > R version 2.11.1 (2010-05-31) > > i386-apple-darwin9.8.0 > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0 gcrma_2.20.0 > > genefilter_1.30.0 affy_1.26.1 Biobase_2.8.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > > Biostrings_2.16.9 DBI_0.2-5 IRanges_1.6.17 > > preprocessCore_1.10.0 > > [8] RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 > > tools_2.11.1 xtable_1.5-6 > > > > Thanks in advance for your help. > > Anjan > > > > > > On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey < > stvjc@channing.harvard.edu> > > wrote: > >> > >> please provide your sessionInfo() and the specific class of array in > >> use -- there are various mouse > >> expression arrays from affy. > >> > >> On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA > >> <anjan.purkayastha@gmail.com> wrote: > >> > Hi, > >> > I have created an affybatch object from 3 cel files. The files have > data > >> > from Affymetrix's Mouse Expression (Oligonucleotide) array. > >> > Affybatch object was created by command: > >> > testAffy <- ReadAffy() > >> > > >> > In the next step I tried to use expresso to adjust background using > RMA > >> > and > >> > normalize using loess, using the command: > >> > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", > >> > normalize.method= "loess") > >> > Here is the output: > >> > background correction: rma > >> > normalization: loess > >> > PM/MM correction : > >> > expression values: > >> > background correcting...done. > >> > normalizing...Done with 1 vs 2 in iteration 1 > >> > Done with 1 vs 3 in iteration 1 > >> > Done with 2 vs 3 in iteration 1 > >> > 1 0.0176947 > >> > done. > >> > Error in function (classes, fdef, mtable) : > >> > unable to find an inherited method for function "computeExprSet", for > >> > signature "AffyBatch", "NULL", "NULL" > >> > > >> > The testAffy.loess object was not created. Any idea why I am getting > an > >> > error on running the expresso command? > >> > Thanks in advance. > >> > Anjan > >> > > >> > -- > >> > =================================== > >> > anjan purkayastha, phd. > >> > research associate > >> > fas center for systems biology, > >> > harvard university > >> > 52 oxford street > >> > cambridge ma 02138 > >> > phone-703.740.6939 > >> > =================================== > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@stat.math.ethz.ch > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > > -- > > =================================== > > anjan purkayastha, phd. > > research associate > > fas center for systems biology, > > harvard university > > 52 oxford street > > cambridge ma 02138 > > phone-703.740.6939 > > =================================== > > > -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]
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On Wed, Oct 6, 2010 at 10:46 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Vince, > Thanks. So it looks like there is no way for me to use expresso to perform > background correction, normalization and then examine the data before > proceeding to other downstream analyses. > Any suggestions on how I can accomplish this without the help of expresso? You can perform standalone background correction using the bg.correct.* functions You can perform normalization at the probe intensity level using the normalize.AffyBatch.* functions these accept and return AffyBatch instances; you can get the intensity measures at any stage using, say, pm() it seems you want to avoid the summarization to an expression value to "examine the data"; expresso expressly wants to do a summarization to an expression value, so don't use it, but use the components separately. > Thanks, > Anjan > > On Wed, Oct 6, 2010 at 10:32 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> > wrote: >> >> I reproduced your experience. ?The problem is that the software lets >> you get away >> with not specifying the summary.method and the pmcorrect.method at the >> interface, but >> when it gets around to doing the expression computations, if it gets >> NULLs (the default) >> it dies. ?expresso() should probably force the user to put something >> in or put reasonable >> defaults. >> >> if you add summary.method = "avgdiff" and pmcorrect.method="pmonly" to >> your call, for example, >> it will complete. ?you have to look over the options for those >> methods; the doc is not crystal >> clear in all places. ?for some parameters function calls will tell you >> the options available >> >> > bgcorrect.methods() >> [1] "bg.correct" "mas" ? ? ? ?"none" ? ? ? "rma" >> > pmcorrect.methods() >> [1] "mas" ? ? ? ?"methods" ? ?"pmonly" ? ? "subtractmm" >> >> summary.methods() does not seem to exist. ?but >> >> > generateExprSet.methods() >> [1] "avgdiff" ? ? ?"liwong" ? ? ? "mas" ? ? ? ? ?"medianpolish" >> "playerout" >> >> seems to supply the relevant options for that parameter. >> >> >> On Wed, Oct 6, 2010 at 9:59 PM, ANJAN PURKAYASTHA >> <anjan.purkayastha at="" gmail.com=""> wrote: >> > Hi Vincent, >> > I used the Mouse Genome 430 2.0 Array >> > >> > (http://www.affymetrix.com/support/technical/byproduct.affx?produ ct=moe430-20) >> > >> > Here is my session info: >> > R version 2.11.1 (2010-05-31) >> > i386-apple-darwin9.8.0 >> > >> > locale: >> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] stats???? graphics? grDevices utils???? datasets? methods?? base >> > >> > other attached packages: >> > [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0? gcrma_2.20.0 >> > genefilter_1.30.0? affy_1.26.1??????? Biobase_2.8.0 >> > >> > loaded via a namespace (and not attached): >> > ?[1] affyio_1.16.0???????? annotate_1.26.1?????? AnnotationDbi_1.10.2 >> > Biostrings_2.16.9???? DBI_0.2-5???????????? IRanges_1.6.17 >> > preprocessCore_1.10.0 >> > ?[8] RSQLite_0.9-2???????? splines_2.11.1??????? survival_2.35-8 >> > tools_2.11.1????????? xtable_1.5-6 >> > >> > Thanks in advance for your help. >> > Anjan >> > >> > >> > On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey >> > <stvjc at="" channing.harvard.edu=""> >> > wrote: >> >> >> >> please provide your sessionInfo() and the specific class of array in >> >> use -- there are various mouse >> >> expression arrays from affy. >> >> >> >> On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA >> >> <anjan.purkayastha at="" gmail.com=""> wrote: >> >> > Hi, >> >> > I have created an affybatch object from 3 cel files. The files have >> >> > data >> >> > from Affymetrix's Mouse Expression (Oligonucleotide) array. >> >> > Affybatch object was created by command: >> >> > testAffy <- ReadAffy() >> >> > >> >> > In the next step I tried to use expresso to adjust background using >> >> > RMA >> >> > and >> >> > normalize using loess, using the command: >> >> > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma", >> >> > normalize.method= "loess") >> >> > Here is the output: >> >> > background correction: rma >> >> > normalization: loess >> >> > PM/MM correction : >> >> > expression values: >> >> > background correcting...done. >> >> > normalizing...Done with 1 vs 2 in iteration 1 >> >> > Done with 1 vs 3 in iteration 1 >> >> > Done with 2 vs 3 in iteration 1 >> >> > 1 0.0176947 >> >> > done. >> >> > Error in function (classes, fdef, mtable) ?: >> >> > ?unable to find an inherited method for function "computeExprSet", >> >> > for >> >> > signature "AffyBatch", "NULL", "NULL" >> >> > >> >> > The testAffy.loess object was not created. ?Any idea why I am getting >> >> > an >> >> > error on running the expresso command? >> >> > Thanks in advance. >> >> > Anjan >> >> > >> >> > -- >> >> > =================================== >> >> > anjan purkayastha, phd. >> >> > research associate >> >> > fas center for systems biology, >> >> > harvard university >> >> > 52 oxford street >> >> > cambridge ma 02138 >> >> > phone-703.740.6939 >> >> > =================================== >> >> > >> >> > ? ? ? ?[[alternative HTML version deleted]] >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> > >> > >> > >> > >> > -- >> > =================================== >> > anjan purkayastha, phd. >> > research associate >> > fas center for systems biology, >> > harvard university >> > 52 oxford street >> > cambridge ma 02138 >> > phone-703.740.6939 >> > =================================== >> > > > > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== >
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