Dear Vladimir thank you for the below message, and sorry for the delayed reply. Your problem is related to this thread: https://stat.ethz.ch/pipermail/bioconductor/2012-March/043888.html I.e. on the short term, to use 'MAList' objects I recommend that you convert them yourself with as( MA, "ExpressionSet") On my to do list: - change arrayQualityMetrics so that it accepts 'MAList' and automatically converts them into 'ExpressionSet'. - make the automatic conversion more tolerant of the different ways that MALists are instantiated by limma. Best wishes Wolfgang Feb/16/12 1:52 PM, Vladimir Krasikov scripsit:: > Dear Wolfgang > > Thanks a lot for your advises. > Bellow I provide error messages for my case > > On Wed, 15 Feb 2012 19:42:27 +0100, Wolfgang Huber <whuber at="" embl.de=""> wrote: > >> Dear Vladimir >> >> Thank you for the feedback and the detailed descriptions. >> >> To remove the reason for the warning from KernSmooth::bkde2D (which is >> called by the MA-plots section), please use the argument >> 'do.logtransform=TRUE' for the function 'arrayQualityMetrics'. Does >> that resolve your problem? > > Thanks, log-transformation indeed resolves warnings. > And also this step brought some meaning to the Report. > >> You say "it doesn't work with MAlist objects at all". Can you please >> provide the exact error message and a reproducible example? > > arrayQualityMetrics(expressionset = MA, outdir = "D:/R2/Out/Report", > force = TRUE, do.logtransform=TRUE) > > The directory 'D:/R2/Out/Report' has been created. > Error in as(expressionset, "NChannelSet") : > no method or default for coercing "MAList" to "NChannelSet" > Error in prepdata(expressionset, intgroup = intgroup, do.logtransform = > do.logtransform) : > Argument 'expressionset' is of class 'MAList', and its automatic > conversion into 'NChannelSet' failed. Please try to convert it manually. > >> Interoperability of 'RGList' and 'MAList' objects with the rest of >> Bioconductor can be challenging. arrayQualityMetrics uses the >> 'convert' package to convert them into 'NChannelSet', and then works >> from that. If you have problems with the phenoData, please send us a >> reproducible example so we can try to update the conversion code. > > I guess pData method is not defined for the RGList (and the MAList) object > and arrayQualityMetrics first tries to set phenoData for the RGList and > then to convert it to the NChannelSet > > pData(RG)$Cy3 <- targets$Cy3 > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for signature > "RGList" > >> As a short term solution to your problem, do the conversion yourself with >> >> library("convert") >> x = as(RG, "NChannelSet") >> >> and then set the phenoData of x as you wish. > > And above solution works perfect and add some colors to otherwise nice > report. > > Thanks a lot > Vladimir > > and as recommended sessionInfo: >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 > LC_MONETARY=Dutch_Netherlands.1252 > [4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] convert_1.30.0 marray_1.32.0 arrayQualityMetrics_3.10.0 Biobase_2.14.0 > [5] limma_3.10.2 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.1 > [5] AnnotationDbi_1.16.16 beadarray_2.4.1 Biostrings_2.22.0 Cairo_1.5-1 > [9] cluster_1.14.2 DBI_0.2-5 genefilter_1.36.0 grid_2.14.1 > [13] Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6 KernSmooth_2.23-7 > [17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0 > RColorBrewer_1.0-5 > [21] RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.1 survival_2.36-12 > [25] SVGAnnotation_0.9-0 tools_2.14.1 vsn_3.22.0 XML_3.9-4.1 > [29] xtable_1.7-0 zlibbioc_1.0.0 > > > > > >> >> best wishes >> Wolfgang >> >> Vladimir Krasikov scripsit 02/15/2012 01:44 PM: >>> Dear list >>> >>> While trying to analyze my data with arrayQualityMetrics (thanks to >>> Axel Klenk for the advise to use it) first on PC and now on MAC. >>> I realize that it is can't run at all on MAC, while on PC it does work, >>> although not as described (or at least not all features described in the >>> vignette are functional) >>> >>> 1. MAC story first: >>> It cann't be loaded without affyPLM (so I guess arrayQualityMetrics >>> DEPENDS on affyPLM, >>> and probably on all other packages which are listed in imports field) >>> >>>> library(arrayQualityMetrics) >>> Creating a generic function for ?boxplot? from package ?graphics? in >>> package ?affyPLM? >>> Creating a generic function for ?hist? from package ?graphics? in >>> package ?affyPLM? >>> Error in as.environment(pos) : >>> no item called "newtable" on the search list >>> In addition: Warning message: >>> In objects(newtable, all.names = TRUE) : >>> ?newtable? converted to character string >>> Error: package/namespace load failed for ?arrayQualityMetrics? >>> >>> MAC sessionInfo: >>>> sessionInfo() >>> R version 2.14.1 (2011-12-22) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] vsn_3.22.0 Biobase_2.14.0 limma_3.10.2 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.32.1 affyio_1.22.0 BiocInstaller_1.2.1 grid_2.14.1 >>> lattice_0.20-0 >>> [6] preprocessCore_1.16.0 tools_2.14.1 zlibbioc_1.0.0 >>>> >>> >>> ################# >>> 2. PC sorry next: >>> >>> Installation also required to install all packages one-by-one from the >>> "imports" >>> >>> I think it doesn't work properly with objects generated by limma (or at >>> least in my case): >>> >>> I did generic import of 61x44K Agilent two-colours microarrays: >>>> RG <- read.maimages(files....) >>> and background correction >>>> RG.b <- backgroundCorrect(RG.raw, method="minimum", offset=50) >>>> arrayQualityMetrics(expressionset = RG.b, outdir = >>>> "D:/R2/Out/Report.61.Rq", force = TRUE) >>> produces 18 warnings of this type: >>>> warnings() >>> 18: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : >>> Binning grid too coarse for current (small) bandwidth: consider >>> increasing 'gridsize' >>> >>> If to create MA from RG with: >MA <- MA.RG(RG.b) >>> >>> It doesn't work with MAlist objects at all, >>> and it is not able to create phenoData for RGlist also (which is quite a >>> pity) >>> [I can't reproduce it on MAC, as I can't start the package at all, >>> I will update this error tomorrow from PC] >>> >>> The rest of the report is generated well for the RG object >>> >>> PC sessionInfo: >>>> sessionInfo() >>> R version 2.14.1 (2011-12-22) >>> Platform: i386-pc-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 >>> [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C >>> [5] LC_TIME=Dutch_Netherlands.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_3.10.0 Biobase_2.14.0 limma_3.10.2 >>> >>> Dear authors of arrayQualityMetrics, may you comment? >>> >>> With kind regards >>> Vladimir >>> >>> >>> >>> >>> >> >> > > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber