Question: Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
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gravatar for Laurent.Pays
5.2 years ago by
Laurent.Pays20
France
Laurent.Pays20 wrote:
Hi to all, After downloading Agilent Data using the ArrayExpress package: >> AEset <-ArrayExpress("E-GEOD-32915?) I verified that AEset was indeed a NChannelSet object: > > class(AEset) > [1] "NChannelSet" > attr(,"package") > [1] ?Biobase" Then I tried to use the arrayQualityMetrics package which should work on NChannelSet objects: > arrayQualityMetrics ( AEset ) But I get this error message: > The report will be written into directory 'arrayQualityMetrics report for AEset'. > Erreur dans platformspecific(expressionset, intgroup, do.logtransform) : > 'assayData(expressionset)' must contain either 'exprs', or 'R' and 'G', but not both. My question is how do I get pass this error, or at least or can I remove either ?exprs?, or ?R? and ?G? from the NChannelSet object knowing that when I try: > > channelNames(AEset) I only get: > [1] "E" ?Eb? and I don?t know what to analyse with arrayQualityMetrics: ?E? or ?Eb?? Thanks in advance to your answers Laurent
ADD COMMENTlink modified 5.2 years ago by Wolfgang Huber13k • written 5.2 years ago by Laurent.Pays20
Answer: Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics pac
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gravatar for Wolfgang Huber
5.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Laurent try with this script: ---------------------- library("ArrayExpress") library("arrayQualityMetrics") library("geneplotter") library("vsn") AEset = ArrayExpress("E-GEOD-32915") ## explore raw data distributions par(mfrow=c(2,1)) for(w in c("E", "Eb")) multidensity(log2(assayData(AEset)[[w]]), main=w) ## normalize v = vsn2(assayData(AEset)$E - assayData(AEset)$Eb) x = ExpressionSet(assayData = exprs(v), phenoData = phenoData(AEset), featureData = featureData(AEset), experimentData = experimentData(AEset)) arrayQualityMetrics ( x, intgroup = "Comment..Sample_source_name." ) ------------------------- Usually, as is here, some data wrangling and ?normalization? is required between downloading a raw data set from ArrayExpress and processing it further with Bioconductor tools. Although the microarray field has been around for a while, these steps are still not fully automated. (Contributions are welcome.) The code above implies the (subjective) decision to subtract Eb from E, and then call vsn2 for between-array ?normalization? and log-like transformation. I then stick the result back into ExpressionSet ?x? and so we go. Hope this helps Wolfgang > print(sessionInfo()) R Under development (unstable) (2014-02-27 r65088) Platform: x86_64-apple-darwin13.0.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] vsn_3.31.2 geneplotter_1.41.1 [3] annotate_1.41.2 AnnotationDbi_1.25.9 [5] lattice_0.20-27 arrayQualityMetrics_3.19.6 [7] ArrayExpress_1.23.1 Biobase_2.23.5 [9] BiocGenerics_0.9.3 fortunes_1.5-2 loaded via a namespace (and not attached): [1] BeadDataPackR_1.15.1 BiocInstaller_1.13.3 Biostrings_2.31.14 [4] Cairo_1.5-5 DBI_0.2-7 Formula_1.1-1 [7] Hmisc_3.14-1 IRanges_1.21.32 KernSmooth_2.23-10 [10] RColorBrewer_1.0-5 RJSONIO_1.0-3 RSQLite_0.11.4 [13] Rcpp_0.11.0 SVGAnnotation_0.93-1 XML_3.98-1.1 [16] XVector_0.3.7 affy_1.41.3 affyPLM_1.39.2 [19] affyio_1.31.0 beadarray_2.13.1 cluster_1.14.4 [22] colorspace_1.2-4 gcrma_2.35.1 genefilter_1.45.1 [25] grid_3.1.0 gridSVG_1.4-0 hwriter_1.3 [28] latticeExtra_0.6-26 limma_3.19.21 plyr_1.8.1 [31] preprocessCore_1.25.5 reshape2_1.2.2 setRNG_2011.11-2 [34] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 [37] survival_2.37-7 xtable_1.7-1 zlibbioc_1.9.0 Il giorno 26 Feb 2014, alle ore 17:43, Laurent.Pays <laurent.pays at="" univ-lyon1.fr=""> ha scritto: > Hi to all, > > After downloading Agilent Data using the ArrayExpress package: > >>> AEset <-ArrayExpress("E-GEOD-32915?) > > I verified that AEset was indeed a NChannelSet object: >>> class(AEset) >> [1] "NChannelSet" >> attr(,"package") >> [1] ?Biobase" > > Then I tried to use the arrayQualityMetrics package which should work on NChannelSet objects: > >> arrayQualityMetrics ( AEset ) > > But I get this error message: > >> The report will be written into directory 'arrayQualityMetrics report for AEset'. >> Erreur dans platformspecific(expressionset, intgroup, do.logtransform) : >> 'assayData(expressionset)' must contain either 'exprs', or 'R' and 'G', but not both. > > My question is how do I get pass this error, or at least or can I remove either ?exprs?, or ?R? and ?G? from the NChannelSet object knowing that when I try: >>> channelNames(AEset) > I only get: >> [1] "E" ?Eb? > and I don?t know what to analyse with arrayQualityMetrics: ?E? or ?Eb?? > > Thanks in advance to your answers > > Laurent > _______________________________________________ > 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 5.2 years ago by Wolfgang Huber13k
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