> hi > i try to make an analysis of a micro array from nimblegen (oligonucleotides > one channel) for example to do a boxplot > i follow the instruction in the pdf "02 - NimbleGen Expression and > Preprocessing" > but i don't know how to make this, with one channel, how can i do ? > > here my code : > > > xys.files <-list.xysfiles(full.names = TRUE) > > xys.files > [1] "./88693_532.xys" "./89430_532.xys" "./96225_532.xys" "./96252_532.xys" > > basename(xys.files) > [1] "88693_532.xys" "89430_532.xys" "96225_532.xys" "96252_532.xys" > > theData <-data.frame(Key = rep(c("cals", "embryon"), each = 2)) > > is.data.frame(theData) > [1] TRUE > > rownames(theData) <- basename(xys.files) > > vm <- data.frame(chanel = factor("_ALL_", levels = c("channel1", > "channel2", "_ALL_")), labelDescription = "oryza sativa") > > pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vm) > > test <-read.xysfiles(xys.files, phenoData = pd) > > when i do this i got the error : > > > test <-read.xysfiles(xys.files, phenoData = pd) > Platform design info loaded. > Checking designs for each XYS file... Done. > Allocating memory... Done. > Reading ./88693_532.xys. > Reading ./89430_532.xys. > Reading ./96225_532.xys. > Reading ./96252_532.xys. > Erreur dans validObject(out) : > invalid class "ExpressionFeatureSet" object: > 'NChannelSet' varMetadata must have a 'channel' column > > > here my session info () : > > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C > [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 > [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8 > [7] LC_PAPER=fr_FR.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.2006.07.24.picaud.dbretro_0.0.1 RSQLite_0.9-2 > [3] DBI_0.2-5 RColorBrewer_1.0-2 > [5] limma_3.4.5 genefilter_1.30.0 > [7] maqcExpression4plex_1.2 oligo_1.12.2 > [9] 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_1.26.1 > [4] AnnotationDbi_1.10.2 Biostrings_2.16.9 IRanges_1.6.17 > [7] preprocessCore_1.10.0 splines_2.11.1 survival_2.35-8 > [10] tools_2.11.1 xtable_1.5-6 > > and my traceback () > > > traceback() > 3: stop(msg, " ", errors, domain = NA) > 2: validObject(out) > 1: read.xysfiles(xys.files, phenoData = pd) > -- > MOZAR Michaël > Master Bioinformatique > Université de Nantes > 0688715937 > -- MOZAR Michaël Master Bioinformatique Université de Nantes 0688715937 [[alternative HTML version deleted]]

you have a typo in your code. you passed 'chanel', where it expected 'channel'. best On 19 October 2010 08:44, Michael MOZAR <mozemaster at="" gmail.com=""> wrote: >> hi >> i try to make an analysis of a micro array from nimblegen (oligonucleotides >> one channel) for example to do a boxplot >> i follow the instruction in the pdf "02 - NimbleGen Expression and >> Preprocessing" >> but i don't know how to make this, ?with one channel, how can i do ? >> >> here my code : >> >> > xys.files <-list.xysfiles(full.names = TRUE) >> > xys.files >> [1] "./88693_532.xys" "./89430_532.xys" "./96225_532.xys" "./96252_532.xys" >> > basename(xys.files) >> [1] "88693_532.xys" "89430_532.xys" "96225_532.xys" "96252_532.xys" >> > theData <-data.frame(Key = rep(c("cals", "embryon"), each = 2)) >> > is.data.frame(theData) >> [1] TRUE >> > rownames(theData) <- basename(xys.files) >> > vm <- data.frame(chanel = factor("_ALL_", levels = c("channel1", >> "channel2", "_ALL_")), labelDescription = "oryza sativa") >> > pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vm) >> > test <-read.xysfiles(xys.files, phenoData = pd) >> >> when i do this i got the error : >> >> > test <-read.xysfiles(xys.files, phenoData = pd) >> Platform design info loaded. >> Checking designs for each XYS file... Done. >> Allocating memory... Done. >> Reading ./88693_532.xys. >> Reading ./89430_532.xys. >> Reading ./96225_532.xys. >> Reading ./96252_532.xys. >> Erreur dans validObject(out) : >> ? invalid class "ExpressionFeatureSet" object: >> ? 'NChannelSet' varMetadata must have a 'channel' column >> >> >> here my session info () : >> >> R version 2.11.1 (2010-05-31) >> x86_64-pc-linux-gnu >> >> locale: >> ?[1] LC_CTYPE=fr_FR.utf8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=fr_FR.utf8 ? ? ? ?LC_COLLATE=fr_FR.utf8 >> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=fr_FR.utf8 >> ?[7] LC_PAPER=fr_FR.utf8 ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> ?[1] pd.2006.07.24.picaud.dbretro_0.0.1 RSQLite_0.9-2 >> ?[3] DBI_0.2-5 ? ? ? ? ? ? ? ? ? ? ? ? ?RColorBrewer_1.0-2 >> ?[5] limma_3.4.5 ? ? ? ? ? ? ? ? ? ? ? ?genefilter_1.30.0 >> ?[7] maqcExpression4plex_1.2 ? ? ? ? ? ?oligo_1.12.2 >> ?[9] 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_1.26.1 >> ?[4] AnnotationDbi_1.10.2 ?Biostrings_2.16.9 ? ? IRanges_1.6.17 >> ?[7] preprocessCore_1.10.0 splines_2.11.1 ? ? ? ?survival_2.35-8 >> [10] tools_2.11.1 ? ? ? ? ?xtable_1.5-6 >> >> and my traceback () >> >> > traceback() >> 3: stop(msg, " ", errors, domain = NA) >> 2: validObject(out) >> 1: read.xysfiles(xys.files, phenoData = pd) >> -- >> MOZAR Micha?l >> Master Bioinformatique >> Universit? de Nantes >> 0688715937 >> > > > > -- > MOZAR Micha?l > Master Bioinformatique > Universit? de Nantes > 0688715937 > > ? ? ? ?[[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 >