Question: exprs() in Bioc 2.10
0
gravatar for Michael Morley
7.5 years ago by
Michael Morley30 wrote:
USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. This code work previously, I basically use it to filter out low expressed genes and control probes. affyGeneFS <- read.celfiles(celFiles,verbose=TRUE) ## Get a list of control probes con <- db(pd.mogene.1.0.st.v1) mainprobes <- dbGetQuery(con, "select DISTINCT transcript_cluster_id from featureSet where type=1 and transcript_cluster_id>1;") mainprobes <- as.character(mainprobes$transcript_cluster_id) eset = rma(affyGeneFS,target='core') apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x > 3.8) ==0 ) FALSE else TRUE ) exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE])), ] The last line gives me: Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == : could not find function "exprs<-" Can I no longer set the expressionset slot this way? Should I be using a different way to begin with? Thanks Mike -- Michael P Morley Senior Bioinformatics Specialist Penn Cardiovascular Institute Translational Research Center,Cubicle 11-114A 3400 Civic Center Blvd, Bldg 421 Philadelphia,PA 19104-5159 Email: mmorley at mail.med.upenn.edu Phone: 215-898-2026
probe affy oligo • 2.0k views
ADD COMMENTlink modified 7.5 years ago by Benilton Carvalho4.3k • written 7.5 years ago by Michael Morley30
Answer: exprs() in Bioc 2.10
0
gravatar for Benilton Carvalho
7.5 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Hi Mike, can you please give the results for sessionInfo() ? it looks like that 'exprs<-' isnt visible for you... benilton On 17 April 2012 21:25, Michael Morley <mmorley at="" mail.med.upenn.edu=""> wrote: > USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. > This code work previously, I basically use it to filter out low expressed > genes and control probes. > > > affyGeneFS <- read.celfiles(celFiles,verbose=TRUE) > > ## Get a list of control probes > con <- db(pd.mogene.1.0.st.v1) > mainprobes <- dbGetQuery(con, "select DISTINCT transcript_cluster_id from > featureSet where type=1 and transcript_cluster_id>1;") > mainprobes <- as.character(mainprobes$transcript_cluster_id) > > > eset = rma(affyGeneFS,target='core') > apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x > 3.8) ==0 ) > FALSE else TRUE ) > > > exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE]) ),] > > The last line gives me: > > Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == > ?: > ?could not find function "exprs<-" > > Can I no longer set the expressionset slot this way? Should I be using a > different way to begin with? > > Thanks > > Mike > > > -- > Michael P Morley > Senior Bioinformatics Specialist > Penn Cardiovascular Institute > Translational Research Center,Cubicle 11-114A > 3400 Civic Center Blvd, Bldg 421 > Philadelphia,PA 19104-5159 > Email: mmorley at mail.med.upenn.edu > Phone: 215-898-2026 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.5 years ago by Benilton Carvalho4.3k
Hi Benilton, One other thing is this command works.. exprs(eset)[1:2,] Here's my sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mogene.1.0.st.v1_3.6.0 RSQLite_0.11.1 DBI_0.2-5 limma_3.12.0 oligo_1.20.1 [6] oligoClasses_1.18.0 loaded via a namespace (and not attached): [1] affxparser_1.28.0 affyio_1.24.0 Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.3 Biostrings_2.24.1 [7] bit_1.1-8 codetools_0.2-8 ff_2.2-6 foreach_1.4.0 IRanges_1.14.2 iterators_1.0.6 [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 tools_2.15.0 zlibbioc_1.2.0 On 04/18/2012 08:04 AM, Benilton Carvalho wrote: > Hi Mike, > > can you please give the results for sessionInfo() ? > > it looks like that 'exprs<-' isnt visible for you... > > benilton > > On 17 April 2012 21:25, Michael Morley<mmorley@mail.med.upenn.edu> wrote: >> USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. >> This code work previously, I basically use it to filter out low expressed >> genes and control probes. >> >> >> affyGeneFS<- read.celfiles(celFiles,verbose=TRUE) >> >> ## Get a list of control probes >> con<- db(pd.mogene.1.0.st.v1) >> mainprobes<- dbGetQuery(con, "select DISTINCT transcript_cluster_id from >> featureSet where type=1 and transcript_cluster_id>1;") >> mainprobes<- as.character(mainprobes$transcript_cluster_id) >> >> >> eset = rma(affyGeneFS,target='core') >> apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x> 3.8) ==0 ) >> FALSE else TRUE ) >> >> >> exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE] )),] >> >> The last line gives me: >> >> Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == >> : >> could not find function "exprs<-" >> >> Can I no longer set the expressionset slot this way? Should I be using a >> different way to begin with? >> >> Thanks >> >> Mike >> >> >> -- >> Michael P Morley >> Senior Bioinformatics Specialist >> Penn Cardiovascular Institute >> Translational Research Center,Cubicle 11-114A >> 3400 Civic Center Blvd, Bldg 421 >> Philadelphia,PA 19104-5159 >> Email: mmorley@mail.med.upenn.edu >> Phone: 215-898-2026 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Michael P Morley Senior Bioinformatics Specialist Penn Cardiovascular Institute Translational Research Center,Cubicle 11-114A 3400 Civic Center Blvd, Bldg 421 Philadelphia,PA 19104-5159 Email: mmorley@mail.med.upenn.edu Phone: 215-898-2026 [[alternative HTML version deleted]]
ADD REPLYlink written 7.5 years ago by Michael Morley30
Hi Mike, I'll work on a permanent solution for this. In the meantime, please load the Biobase package explicitly, as in: library(Biobase) library(oligo) and everything should work as expected. b On 18 April 2012 13:56, Michael Morley <mmorley at="" mail.med.upenn.edu=""> wrote: > Hi Benilton, > > One other thing is this command works.. > > exprs(eset)[1:2,] > > > > > Here's my sessionInfo() > > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C > LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8 > LC_MONETARY=en_US.UTF-8 > ?[6] LC_MESSAGES=en_US.UTF-8??? LC_PAPER=C > LC_NAME=C????????????????? LC_ADDRESS=C > LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > other attached packages: > [1] pd.mogene.1.0.st.v1_3.6.0 RSQLite_0.11.1 > DBI_0.2-5???????????????? limma_3.12.0????????????? oligo_1.20.1 > [6] oligoClasses_1.18.0 > > loaded via a namespace (and not attached): > ?[1] affxparser_1.28.0???? affyio_1.24.0???????? Biobase_2.16.0 > BiocGenerics_0.2.0??? BiocInstaller_1.4.3?? Biostrings_2.24.1 > ?[7] bit_1.1-8???????????? codetools_0.2-8?????? ff_2.2-6 > foreach_1.4.0???????? IRanges_1.14.2??????? iterators_1.0.6 > [13] preprocessCore_1.18.0 splines_2.15.0??????? stats4_2.15.0 > tools_2.15.0????????? zlibbioc_1.2.0 > > > > On 04/18/2012 08:04 AM, Benilton Carvalho wrote: > > Hi Mike, > > can you please give the results for sessionInfo() ? > > it looks like that 'exprs<-' isnt visible for you... > > benilton > > On 17 April 2012 21:25, Michael Morley <mmorley at="" mail.med.upenn.edu=""> wrote: > > USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. > This code work previously, I basically use it to filter out low expressed > genes and control probes. > > > affyGeneFS <- read.celfiles(celFiles,verbose=TRUE) > > ## Get a list of control probes > con <- db(pd.mogene.1.0.st.v1) > mainprobes <- dbGetQuery(con, "select DISTINCT transcript_cluster_id from > featureSet where type=1 and transcript_cluster_id>1;") > mainprobes <- as.character(mainprobes$transcript_cluster_id) > > > eset = rma(affyGeneFS,target='core') > apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x > 3.8) ==0 ) > FALSE else TRUE ) > > > exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE]) ),] > > The last line gives me: > > Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == > ?: > ?could not find function "exprs<-" > > Can I no longer set the expressionset slot this way? Should I be using a > different way to begin with? > > Thanks > > Mike > > > -- > Michael P Morley > Senior Bioinformatics Specialist > Penn Cardiovascular Institute > Translational Research Center,Cubicle 11-114A > 3400 Civic Center Blvd, Bldg 421 > Philadelphia,PA 19104-5159 > Email: mmorley at mail.med.upenn.edu > Phone: 215-898-2026 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Michael P Morley > Senior Bioinformatics Specialist > Penn Cardiovascular Institute > Translational Research Center,Cubicle 11-114A > 3400 Civic Center Blvd, Bldg 421 > Philadelphia,PA 19104-5159 > Email: mmorley at mail.med.upenn.edu > Phone: 215-898-2026
ADD REPLYlink written 7.5 years ago by Benilton Carvalho4.3k
Perfect! Thank you. On 04/18/2012 09:03 AM, Benilton Carvalho wrote: > Hi Mike, > > I'll work on a permanent solution for this. In the meantime, please > load the Biobase package explicitly, as in: > > library(Biobase) > library(oligo) > > and everything should work as expected. > > b > > On 18 April 2012 13:56, Michael Morley<mmorley at="" mail.med.upenn.edu=""> wrote: >> Hi Benilton, >> >> One other thing is this command works.. >> >> exprs(eset)[1:2,] >> >> >> >> >> Here's my sessionInfo() >> >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 >> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C >> LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.mogene.1.0.st.v1_3.6.0 RSQLite_0.11.1 >> DBI_0.2-5 limma_3.12.0 oligo_1.20.1 >> [6] oligoClasses_1.18.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.28.0 affyio_1.24.0 Biobase_2.16.0 >> BiocGenerics_0.2.0 BiocInstaller_1.4.3 Biostrings_2.24.1 >> [7] bit_1.1-8 codetools_0.2-8 ff_2.2-6 >> foreach_1.4.0 IRanges_1.14.2 iterators_1.0.6 >> [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 >> tools_2.15.0 zlibbioc_1.2.0 >> >> >> >> On 04/18/2012 08:04 AM, Benilton Carvalho wrote: >> >> Hi Mike, >> >> can you please give the results for sessionInfo() ? >> >> it looks like that 'exprs<-' isnt visible for you... >> >> benilton >> >> On 17 April 2012 21:25, Michael Morley<mmorley at="" mail.med.upenn.edu=""> wrote: >> >> USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. >> This code work previously, I basically use it to filter out low expressed >> genes and control probes. >> >> >> affyGeneFS<- read.celfiles(celFiles,verbose=TRUE) >> >> ## Get a list of control probes >> con<- db(pd.mogene.1.0.st.v1) >> mainprobes<- dbGetQuery(con, "select DISTINCT transcript_cluster_id from >> featureSet where type=1 and transcript_cluster_id>1;") >> mainprobes<- as.character(mainprobes$transcript_cluster_id) >> >> >> eset = rma(affyGeneFS,target='core') >> apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x> 3.8) ==0 ) >> FALSE else TRUE ) >> >> >> exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE] )),] >> >> The last line gives me: >> >> Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == >> : >> could not find function "exprs<-" >> >> Can I no longer set the expressionset slot this way? Should I be using a >> different way to begin with? >> >> Thanks >> >> Mike >> >> >> -- >> Michael P Morley >> Senior Bioinformatics Specialist >> Penn Cardiovascular Institute >> Translational Research Center,Cubicle 11-114A >> 3400 Civic Center Blvd, Bldg 421 >> Philadelphia,PA 19104-5159 >> Email: mmorley at mail.med.upenn.edu >> Phone: 215-898-2026 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Michael P Morley >> Senior Bioinformatics Specialist >> Penn Cardiovascular Institute >> Translational Research Center,Cubicle 11-114A >> 3400 Civic Center Blvd, Bldg 421 >> Philadelphia,PA 19104-5159 >> Email: mmorley at mail.med.upenn.edu >> Phone: 215-898-2026 -- Michael P Morley Senior Bioinformatics Specialist Penn Cardiovascular Institute Translational Research Center,Cubicle 11-114A 3400 Civic Center Blvd, Bldg 421 Philadelphia,PA 19104-5159 Email: mmorley at mail.med.upenn.edu Phone: 215-898-2026
ADD REPLYlink written 7.5 years ago by Michael Morley30
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