boxplot error with expression set using oligo package and Human gene st 1.0 arrays
1
0
Entering edit mode
jos matejus ▴ 30
@jos-matejus-3848
Last seen 6.9 years ago
Dear All, I was wondering whether anyone could help decipher an error message I am getting when I try to plot a boxplot of normalised expression values using the oligo package for human gene st 1.0 arrays. Here is the code I am using: library(oligo) library(limma) library(genefilter) library(pd.hugene.1.0.st.v1) library(hugene10sttranscriptcluster.db) cel.dir <- "C:/cel files" cel.files <- list.celfiles(cel.dir, full.names=TRUE) #construct some phenodata theData <- data.frame(Key=rep(c("VitC", "Control"), each=3)) rownames(theData) <- basename(cel.files) vMtData <- data.frame(channel = factor("_ALL_", levels = c("channel1", "channel2", "_ALL_")), labelDescription = "Sample treatment") pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vMtData) affyData<-read.celfiles(cel.files, pkgname="pd.hugene.1.0.st.v1", phenoData=pd) eset <- rma(affyData, target="core") show(eset) #ExpressionSet (storageMode: lockedEnvironment) #assayData: 33297 features, 6 samples # element names: exprs #protocolData: none #phenoData # rowNames: RB1_A1_140, RB2_A2_14010, ..., RB6_C3_10 ?(6 total) #varLabels and varMetadata description: # ?Key: Sample treatment # ?additional varMetadata: channel #featureData: none #experimentData: use 'experimentData(object)' #Annotation: pd.hugene.1.0.st.v1 boxplot(eset, transfo = identity, main = "After RMA") #Error in .local(x, ...) : object 'nsamples' not found I noticed a similar problem was reported in the archives at: http://thread.gmane.org/gmane.science.biology.informatics.conductor/29 047/focus=29050 however, I am still receiving this error message despite using version 1.12.1 of the oligo package. I have also used: boxplot(exprs(eset)) as suggested by Mike Smith (http://thread.gmane.org/gmane.science.biology.informatics.conductor/2 9047/focus=29050) but this seems to indicate a large number of outliers which I dont get when plotting before normailsation and also when using the arrayQualityMetrics package on post processed values. arrayQualityMetrics(expressionset = eset) Any help would be gratefully received. Best Jos sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1 AnnotationDbi_1.10.1 [4] pd.hugene.1.0.st.v1_3.0.1 RSQLite_0.9-1 DBI_0.2-5 [7] genefilter_1.30.0 limma_3.4.1 oligo_1.12.1 [10] oligoClasses_1.10.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affxparser_1.20.0 affyio_1.16.0 annotate_1.26.0 Biostrings_2.16.2 IRanges_1.6.4 [6] preprocessCore_1.10.0 splines_2.11.0 survival_2.35-8 xtable_1.5-6
oligo DECIPHER oligo DECIPHER • 1.2k views
ADD COMMENT
0
Entering edit mode
@benilton-carvalho-1375
Last seen 16 months ago
Brazil/Campinas/UNICAMP
Dear Jos, thanks for the report. I've just fixed the "object 'nsamples' not found" error on oligo version 1.12.2, which should be available for download in about 1 day or so. In the meantime, the plot you want to look at is: tmp = exprs(eset) tmp = as.data.frame(tmp) boxplot(tmp, range=0) best, b On 7 June 2010 10:04, jos matejus <matejus106 at="" googlemail.com=""> wrote: > Dear All, > > I was wondering whether anyone could help decipher an error message I > am getting when I try to plot a boxplot of normalised expression > values using the oligo package for human gene st 1.0 arrays. Here is > the code I am using: > > library(oligo) > library(limma) > library(genefilter) > library(pd.hugene.1.0.st.v1) > library(hugene10sttranscriptcluster.db) > > cel.dir <- "C:/cel files" > cel.files <- list.celfiles(cel.dir, full.names=TRUE) > > #construct some phenodata > theData <- data.frame(Key=rep(c("VitC", "Control"), each=3)) > rownames(theData) <- basename(cel.files) > > vMtData <- data.frame(channel = factor("_ALL_", > levels = c("channel1", "channel2", > "_ALL_")), labelDescription = "Sample treatment") > > pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vMtData) > > affyData<-read.celfiles(cel.files, pkgname="pd.hugene.1.0.st.v1", phenoData=pd) > > eset <- rma(affyData, target="core") > > show(eset) > #ExpressionSet (storageMode: lockedEnvironment) > #assayData: 33297 features, 6 samples > # element names: exprs > #protocolData: none > #phenoData > # rowNames: RB1_A1_140, RB2_A2_14010, ..., RB6_C3_10 ?(6 total) > #varLabels and varMetadata description: > # ?Key: Sample treatment > # ?additional varMetadata: channel > #featureData: none > #experimentData: use 'experimentData(object)' > #Annotation: pd.hugene.1.0.st.v1 > > boxplot(eset, transfo = identity, main = "After RMA") > > #Error in .local(x, ...) : object 'nsamples' not found > > I noticed a similar problem was reported in the archives at: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 29047/focus=29050 > > however, I am still receiving this error message despite using version > 1.12.1 of the oligo package. I have also used: > > boxplot(exprs(eset)) > > as suggested by Mike Smith > (http://thread.gmane.org/gmane.science.biology.informatics.conductor /29047/focus=29050) > > but this seems to indicate a large number of outliers which I dont get > when plotting before normailsation and also when using the > arrayQualityMetrics package on post processed values. > > arrayQualityMetrics(expressionset = eset) > > Any help would be gratefully received. > Best > Jos > > sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 ?LC_CTYPE=English_United > Kingdom.1252 ? ?LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? ?LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1 > ? ? ? ?AnnotationDbi_1.10.1 > ?[4] pd.hugene.1.0.st.v1_3.0.1 ? ? ? ? ? ?RSQLite_0.9-1 > ? ? ? ?DBI_0.2-5 > ?[7] genefilter_1.30.0 ? ? ? ? ? ? ? ? ? ?limma_3.4.1 > ? ? ? ?oligo_1.12.1 > [10] oligoClasses_1.10.0 ? ? ? ? ? ? ? ? ?Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.20.0 ? ? affyio_1.16.0 ? ? ? ? annotate_1.26.0 > Biostrings_2.16.2 ? ? IRanges_1.6.4 > [6] preprocessCore_1.10.0 splines_2.11.0 ? ? ? ?survival_2.35-8 > xtable_1.5-6 > > _______________________________________________ > 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 >
ADD COMMENT

Login before adding your answer.

Traffic: 432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6