error with pd.ragene1.0.st.v1 and oligo
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Hi, I am analyzing some rat arrays. I get this error: Error in validObject(.Object) : invalid class ???GeneFeatureSet??? object: featureNames differ between assayData and featureData Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> validObject I am pretty sure my code is close to correct as I put together this script to analyze the pd.rat230.2 arrays for another project and it worked great. Now I have switched to a project that used the pd.ragene.1.0.st.v1 instead and now I am getting this error and am in need of figuring it out again. Any pointers would be great. Thanks, Ian -- output of sessionInfo(): > datadir <- "in_vitro_rat" > setwd(datadir) > > celFiles <- list.celfiles() > exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") Platform design info loaded. Reading in : 10.CEL Reading in : 11.CEL Reading in : 12.CEL Reading in : 13.CEL Reading in : 14.CEL Reading in : 15.CEL Reading in : 16.CEL Reading in : 17.CEL Reading in : 18.CEL Reading in : 19.CEL Reading in : 1.CEL Reading in : 20.CEL Reading in : 21.CEL Reading in : 22.CEL Reading in : 23.CEL Reading in : 24.CEL Reading in : 2.CEL Reading in : 3.CEL Reading in : 4.CEL Reading in : 5.CEL Reading in : 6.CEL Reading in : 7.CEL Reading in : 8.CEL Reading in : 9.CEL > png(file="exp.hist.png",width = 500, height = 600, type = "cairo") > hist(exp_data) Error in validObject(.Object) : invalid class ???GeneFeatureSet??? object: featureNames differ between assayData and featureData Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> validObject Execution halted -- Sent via the guest posting facility at bioconductor.org.
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@ian-b-stanaway-6402
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Hi, I should also note that if I remove the hist and boxplot sections of the script if proceeds and calculates all the normalizations, design, contrast.matrix and outputs topTables just fine. It seems the naming in the graphical functions underlying code is off. best, Ian On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > > I am analyzing some rat arrays. I get this error: > > Error in validObject(.Object) : > invalid class "GeneFeatureSet" object: featureNames differ between assayData and featureData > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> validObject > > I am pretty sure my code is close to correct as I put together this script to analyze the pd.rat230.2 arrays for another project and it worked great. > > Now I have switched to a project that used the pd.ragene.1.0.st.v1 instead and now I am getting this error and am in need of figuring it out again. > > Any pointers would be great. > > Thanks, > > Ian > > -- output of sessionInfo(): > >> datadir <- "in_vitro_rat" >> setwd(datadir) >> >> celFiles <- list.celfiles() >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") > Platform design info loaded. > Reading in : 10.CEL > Reading in : 11.CEL > Reading in : 12.CEL > Reading in : 13.CEL > Reading in : 14.CEL > Reading in : 15.CEL > Reading in : 16.CEL > Reading in : 17.CEL > Reading in : 18.CEL > Reading in : 19.CEL > Reading in : 1.CEL > Reading in : 20.CEL > Reading in : 21.CEL > Reading in : 22.CEL > Reading in : 23.CEL > Reading in : 24.CEL > Reading in : 2.CEL > Reading in : 3.CEL > Reading in : 4.CEL > Reading in : 5.CEL > Reading in : 6.CEL > Reading in : 7.CEL > Reading in : 8.CEL > Reading in : 9.CEL >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") >> hist(exp_data) > Error in validObject(.Object) : > invalid class "GeneFeatureSet" object: featureNames differ between assayData and featureData > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> validObject > Execution halted > > > -- > Sent via the guest posting facility at bioconductor.org.
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Ian, I'm working on a fix, which should be available in the next couple of days. Benilton On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard@uw.edu> wrote: > Hi, > > I should also note that if I remove the hist and boxplot sections of > the script if proceeds and calculates all the normalizations, design, > contrast.matrix and outputs topTables just fine. It seems the naming > in the graphical functions underlying code is off. > > best, > > Ian > > On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest@bioconductor.org> > wrote: > > > > Hi, > > > > I am analyzing some rat arrays. I get this error: > > > > Error in validObject(.Object) : > > invalid class "GeneFeatureSet" object: featureNames differ between > assayData and featureData > > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > validObject > > > > I am pretty sure my code is close to correct as I put together this > script to analyze the pd.rat230.2 arrays for another project and it worked > great. > > > > Now I have switched to a project that used the pd.ragene.1.0.st.v1 > instead and now I am getting this error and am in need of figuring it out > again. > > > > Any pointers would be great. > > > > Thanks, > > > > Ian > > > > -- output of sessionInfo(): > > > >> datadir <- "in_vitro_rat" > >> setwd(datadir) > >> > >> celFiles <- list.celfiles() > >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") > > Platform design info loaded. > > Reading in : 10.CEL > > Reading in : 11.CEL > > Reading in : 12.CEL > > Reading in : 13.CEL > > Reading in : 14.CEL > > Reading in : 15.CEL > > Reading in : 16.CEL > > Reading in : 17.CEL > > Reading in : 18.CEL > > Reading in : 19.CEL > > Reading in : 1.CEL > > Reading in : 20.CEL > > Reading in : 21.CEL > > Reading in : 22.CEL > > Reading in : 23.CEL > > Reading in : 24.CEL > > Reading in : 2.CEL > > Reading in : 3.CEL > > Reading in : 4.CEL > > Reading in : 5.CEL > > Reading in : 6.CEL > > Reading in : 7.CEL > > Reading in : 8.CEL > > Reading in : 9.CEL > >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") > >> hist(exp_data) > > Error in validObject(.Object) : > > invalid class "GeneFeatureSet" object: featureNames differ between > assayData and featureData > > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > validObject > > Execution halted > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Many Thanks! On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Ian, I'm working on a fix, which should be available in the next couple of > days. Benilton > > On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard at="" uw.edu=""> wrote: >> >> Hi, >> >> I should also note that if I remove the hist and boxplot sections of >> the script if proceeds and calculates all the normalizations, design, >> contrast.matrix and outputs topTables just fine. It seems the naming >> in the graphical functions underlying code is off. >> >> best, >> >> Ian >> >> On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest at="" bioconductor.org=""> >> wrote: >> > >> > Hi, >> > >> > I am analyzing some rat arrays. I get this error: >> > >> > Error in validObject(.Object) : >> > invalid class "GeneFeatureSet" object: featureNames differ between >> > assayData and featureData >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> >> > validObject >> > >> > I am pretty sure my code is close to correct as I put together this >> > script to analyze the pd.rat230.2 arrays for another project and it worked >> > great. >> > >> > Now I have switched to a project that used the pd.ragene.1.0.st.v1 >> > instead and now I am getting this error and am in need of figuring it out >> > again. >> > >> > Any pointers would be great. >> > >> > Thanks, >> > >> > Ian >> > >> > -- output of sessionInfo(): >> > >> >> datadir <- "in_vitro_rat" >> >> setwd(datadir) >> >> >> >> celFiles <- list.celfiles() >> >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") >> > Platform design info loaded. >> > Reading in : 10.CEL >> > Reading in : 11.CEL >> > Reading in : 12.CEL >> > Reading in : 13.CEL >> > Reading in : 14.CEL >> > Reading in : 15.CEL >> > Reading in : 16.CEL >> > Reading in : 17.CEL >> > Reading in : 18.CEL >> > Reading in : 19.CEL >> > Reading in : 1.CEL >> > Reading in : 20.CEL >> > Reading in : 21.CEL >> > Reading in : 22.CEL >> > Reading in : 23.CEL >> > Reading in : 24.CEL >> > Reading in : 2.CEL >> > Reading in : 3.CEL >> > Reading in : 4.CEL >> > Reading in : 5.CEL >> > Reading in : 6.CEL >> > Reading in : 7.CEL >> > Reading in : 8.CEL >> > Reading in : 9.CEL >> >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") >> >> hist(exp_data) >> > Error in validObject(.Object) : >> > invalid class "GeneFeatureSet" object: featureNames differ between >> > assayData and featureData >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> >> > validObject >> > Execution halted >> > >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org.
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Hi Benilton, I am also trying to use this probe id database to assign gene symbols to probe ids and it seems that most of the probe ids in the 'correct' db are not shared with this chip. Do you think there is a revision problem with this array db also? ragene10stprobeset.db probeset.list <-featureNames(exp_data_rma) xtmp <- ragene10stprobesetSYMBOL mappedprobes <- mappedkeys(xtmp) genes.symbols <- as.list(xtmp[mappedprobes]) xtmp <- paste(probeset.list, mappedprobes, genes.symbols, genes.refseqNMids, collapse="\n") write.table(t(xtmp), file="nm_id_lookup", row.names=F, col.names=FALSE, sep="\t", quote=FALSE) then when I look at the list the 2 for columns should be matching probe ids but they don't match: 10700965 10703255 Zswim5 c("NM_001107963", "NP_001101433") 10700966 10703266 RGD1561339 c("XM_577732", "XP_577732") 10700967 10703267 RGD1564858 c("XM_233450", "XP_233450") 10700968 10703268 RGD1564858 c("XM_233450", "XP_233450") 10700969 10703303 RGD1560972 c("XM_577704", "XP_577704") 10700970 10703304 RGD1560808 c("XM_577734", "XP_577734") 10700971 10703311 Smoc2 c("NM_001106215", "NP_001099685") 10700972 10703312 Smoc2 c("NM_001106215", "NP_001099685") 10700973 10703313 Smoc2 c("NM_001106215", "NP_001099685") 10700974 10703314 Smoc2 c("NM_001106215", "NP_001099685") #if I leave this in it gobbles up memory gene.info.tmp <- data.frame(probeset.list=probeset.list, genes.symbols=genes.symbols, stringsAsFactors=F) thanks, Ian On Wed, Feb 12, 2014 at 11:46 AM, Ian B Stanaway <bard at="" uw.edu=""> wrote: > Many Thanks! > > On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> Ian, I'm working on a fix, which should be available in the next couple of >> days. Benilton >> >> On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard at="" uw.edu=""> wrote: >>> >>> Hi, >>> >>> I should also note that if I remove the hist and boxplot sections of >>> the script if proceeds and calculates all the normalizations, design, >>> contrast.matrix and outputs topTables just fine. It seems the naming >>> in the graphical functions underlying code is off. >>> >>> best, >>> >>> Ian >>> >>> On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest at="" bioconductor.org=""> >>> wrote: >>> > >>> > Hi, >>> > >>> > I am analyzing some rat arrays. I get this error: >>> > >>> > Error in validObject(.Object) : >>> > invalid class "GeneFeatureSet" object: featureNames differ between >>> > assayData and featureData >>> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> >>> > validObject >>> > >>> > I am pretty sure my code is close to correct as I put together this >>> > script to analyze the pd.rat230.2 arrays for another project and it worked >>> > great. >>> > >>> > Now I have switched to a project that used the pd.ragene.1.0.st.v1 >>> > instead and now I am getting this error and am in need of figuring it out >>> > again. >>> > >>> > Any pointers would be great. >>> > >>> > Thanks, >>> > >>> > Ian >>> > >>> > -- output of sessionInfo(): >>> > >>> >> datadir <- "in_vitro_rat" >>> >> setwd(datadir) >>> >> >>> >> celFiles <- list.celfiles() >>> >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") >>> > Platform design info loaded. >>> > Reading in : 10.CEL >>> > Reading in : 11.CEL >>> > Reading in : 12.CEL >>> > Reading in : 13.CEL >>> > Reading in : 14.CEL >>> > Reading in : 15.CEL >>> > Reading in : 16.CEL >>> > Reading in : 17.CEL >>> > Reading in : 18.CEL >>> > Reading in : 19.CEL >>> > Reading in : 1.CEL >>> > Reading in : 20.CEL >>> > Reading in : 21.CEL >>> > Reading in : 22.CEL >>> > Reading in : 23.CEL >>> > Reading in : 24.CEL >>> > Reading in : 2.CEL >>> > Reading in : 3.CEL >>> > Reading in : 4.CEL >>> > Reading in : 5.CEL >>> > Reading in : 6.CEL >>> > Reading in : 7.CEL >>> > Reading in : 8.CEL >>> > Reading in : 9.CEL >>> >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") >>> >> hist(exp_data) >>> > Error in validObject(.Object) : >>> > invalid class "GeneFeatureSet" object: featureNames differ between >>> > assayData and featureData >>> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> >>> > validObject >>> > Execution halted >>> > >>> > >>> > -- >>> > Sent via the guest posting facility at bioconductor.org.
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Hi Ian, I'm not sure how exp_data_rma was created... Also, the .db package you refer to is not maintained by me... So, my help here is quite limited. On my example below, 'y' is the result of rma()... something like: x = read.celfiles(list.celfiles()) y = rma(x) The 'y' variable above contains the result at the transcript level. So, I'd use the ragene10sttranscriptcluster.db package... And my attempt would look like: library(ragene10sttranscriptcluster.db) psn <- featureNames(y) refseq <- as.list(ragene10sttranscriptclusterREFSEQ[psn]) symbol <- as.list(ragene10sttranscriptclusterSYMBOL[psn]) refseq <- sapply(refseq, paste, collapse=';') refseq[refseq=='NA'] <- NA symbol <- sapply(symbol, paste, collapse=';') symbol[symbol=='NA'] <- NA annot <- data.frame(probeset=psn, refseq=refseq, symbol=symbol) Alternatively, I'd explore: ## loads info from affymetrix files featureData(y) = getNetAffx(y, 'transcript') benilton 2014-02-12 19:44 GMT-02:00 Ian B Stanaway <bard@uw.edu>: > Hi Benilton, > > I am also trying to use this probe id database to assign gene symbols > to probe ids and it seems that most of the probe ids in the 'correct' > db are not shared with this chip. Do you think there is a revision > problem with this array db also? > > ragene10stprobeset.db > > probeset.list <-featureNames(exp_data_rma) > xtmp <- ragene10stprobesetSYMBOL > mappedprobes <- mappedkeys(xtmp) > genes.symbols <- as.list(xtmp[mappedprobes]) > xtmp <- paste(probeset.list, mappedprobes, genes.symbols, > genes.refseqNMids, collapse="\n") > write.table(t(xtmp), file="nm_id_lookup", row.names=F, > col.names=FALSE, sep="\t", quote=FALSE) > > then when I look at the list the 2 for columns should be matching > probe ids but they don't match: > > 10700965 10703255 Zswim5 c("NM_001107963", "NP_001101433") > 10700966 10703266 RGD1561339 c("XM_577732", "XP_577732") > 10700967 10703267 RGD1564858 c("XM_233450", "XP_233450") > 10700968 10703268 RGD1564858 c("XM_233450", "XP_233450") > 10700969 10703303 RGD1560972 c("XM_577704", "XP_577704") > 10700970 10703304 RGD1560808 c("XM_577734", "XP_577734") > 10700971 10703311 Smoc2 c("NM_001106215", "NP_001099685") > 10700972 10703312 Smoc2 c("NM_001106215", "NP_001099685") > 10700973 10703313 Smoc2 c("NM_001106215", "NP_001099685") > 10700974 10703314 Smoc2 c("NM_001106215", "NP_001099685") > > > #if I leave this in it gobbles up memory > gene.info.tmp <- data.frame(probeset.list=probeset.list, > genes.symbols=genes.symbols, stringsAsFactors=F) > > thanks, > > Ian > > > On Wed, Feb 12, 2014 at 11:46 AM, Ian B Stanaway <bard@uw.edu> wrote: > > Many Thanks! > > > > On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho > > <beniltoncarvalho@gmail.com> wrote: > >> Ian, I'm working on a fix, which should be available in the next couple > of > >> days. Benilton > >> > >> On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard@uw.edu> wrote: > >>> > >>> Hi, > >>> > >>> I should also note that if I remove the hist and boxplot sections of > >>> the script if proceeds and calculates all the normalizations, design, > >>> contrast.matrix and outputs topTables just fine. It seems the naming > >>> in the graphical functions underlying code is off. > >>> > >>> best, > >>> > >>> Ian > >>> > >>> On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest@bioconductor.org> > >>> wrote: > >>> > > >>> > Hi, > >>> > > >>> > I am analyzing some rat arrays. I get this error: > >>> > > >>> > Error in validObject(.Object) : > >>> > invalid class "GeneFeatureSet" object: featureNames differ between > >>> > assayData and featureData > >>> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > >>> > validObject > >>> > > >>> > I am pretty sure my code is close to correct as I put together this > >>> > script to analyze the pd.rat230.2 arrays for another project and it > worked > >>> > great. > >>> > > >>> > Now I have switched to a project that used the pd.ragene.1.0.st.v1 > >>> > instead and now I am getting this error and am in need of figuring > it out > >>> > again. > >>> > > >>> > Any pointers would be great. > >>> > > >>> > Thanks, > >>> > > >>> > Ian > >>> > > >>> > -- output of sessionInfo(): > >>> > > >>> >> datadir <- "in_vitro_rat" > >>> >> setwd(datadir) > >>> >> > >>> >> celFiles <- list.celfiles() > >>> >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") > >>> > Platform design info loaded. > >>> > Reading in : 10.CEL > >>> > Reading in : 11.CEL > >>> > Reading in : 12.CEL > >>> > Reading in : 13.CEL > >>> > Reading in : 14.CEL > >>> > Reading in : 15.CEL > >>> > Reading in : 16.CEL > >>> > Reading in : 17.CEL > >>> > Reading in : 18.CEL > >>> > Reading in : 19.CEL > >>> > Reading in : 1.CEL > >>> > Reading in : 20.CEL > >>> > Reading in : 21.CEL > >>> > Reading in : 22.CEL > >>> > Reading in : 23.CEL > >>> > Reading in : 24.CEL > >>> > Reading in : 2.CEL > >>> > Reading in : 3.CEL > >>> > Reading in : 4.CEL > >>> > Reading in : 5.CEL > >>> > Reading in : 6.CEL > >>> > Reading in : 7.CEL > >>> > Reading in : 8.CEL > >>> > Reading in : 9.CEL > >>> >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") > >>> >> hist(exp_data) > >>> > Error in validObject(.Object) : > >>> > invalid class "GeneFeatureSet" object: featureNames differ between > >>> > assayData and featureData > >>> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > >>> > validObject > >>> > Execution halted > >>> > > >>> > > >>> > -- > >>> > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Hi Ian, you should look for version 1.26.2 in the next few days. b 2014-02-12 17:46 GMT-02:00 Ian B Stanaway <bard@uw.edu>: > Many Thanks! > > On Wed, Feb 12, 2014 at 11:39 AM, Benilton Carvalho > <beniltoncarvalho@gmail.com> wrote: > > Ian, I'm working on a fix, which should be available in the next couple > of > > days. Benilton > > > > On Feb 12, 2014 4:25 PM, "Ian B Stanaway" <bard@uw.edu> wrote: > >> > >> Hi, > >> > >> I should also note that if I remove the hist and boxplot sections of > >> the script if proceeds and calculates all the normalizations, design, > >> contrast.matrix and outputs topTables just fine. It seems the naming > >> in the graphical functions underlying code is off. > >> > >> best, > >> > >> Ian > >> > >> On Tue, Feb 11, 2014 at 1:59 PM, Ian [guest] <guest@bioconductor.org> > >> wrote: > >> > > >> > Hi, > >> > > >> > I am analyzing some rat arrays. I get this error: > >> > > >> > Error in validObject(.Object) : > >> > invalid class "GeneFeatureSet" object: featureNames differ between > >> > assayData and featureData > >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > >> > validObject > >> > > >> > I am pretty sure my code is close to correct as I put together this > >> > script to analyze the pd.rat230.2 arrays for another project and it > worked > >> > great. > >> > > >> > Now I have switched to a project that used the pd.ragene.1.0.st.v1 > >> > instead and now I am getting this error and am in need of figuring it > out > >> > again. > >> > > >> > Any pointers would be great. > >> > > >> > Thanks, > >> > > >> > Ian > >> > > >> > -- output of sessionInfo(): > >> > > >> >> datadir <- "in_vitro_rat" > >> >> setwd(datadir) > >> >> > >> >> celFiles <- list.celfiles() > >> >> exp_data <- read.celfiles(celFiles, pkgname="pd.ragene.1.0.st.v1") > >> > Platform design info loaded. > >> > Reading in : 10.CEL > >> > Reading in : 11.CEL > >> > Reading in : 12.CEL > >> > Reading in : 13.CEL > >> > Reading in : 14.CEL > >> > Reading in : 15.CEL > >> > Reading in : 16.CEL > >> > Reading in : 17.CEL > >> > Reading in : 18.CEL > >> > Reading in : 19.CEL > >> > Reading in : 1.CEL > >> > Reading in : 20.CEL > >> > Reading in : 21.CEL > >> > Reading in : 22.CEL > >> > Reading in : 23.CEL > >> > Reading in : 24.CEL > >> > Reading in : 2.CEL > >> > Reading in : 3.CEL > >> > Reading in : 4.CEL > >> > Reading in : 5.CEL > >> > Reading in : 6.CEL > >> > Reading in : 7.CEL > >> > Reading in : 8.CEL > >> > Reading in : 9.CEL > >> >> png(file="exp.hist.png",width = 500, height = 600, type = "cairo") > >> >> hist(exp_data) > >> > Error in validObject(.Object) : > >> > invalid class "GeneFeatureSet" object: featureNames differ between > >> > assayData and featureData > >> > Calls: hist ... assayData<- -> assayData<- -> .init_NChannelSet -> > >> > validObject > >> > Execution halted > >> > > >> > > >> > -- > >> > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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