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Question: arrayQualityMetrics package - bugs and errors
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gravatar for Vladimir Krasikov
6.5 years ago by
Vladimir Krasikov90 wrote:
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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
ADD COMMENTlink modified 6.5 years ago by Wolfgang Huber13k • written 6.5 years ago by Vladimir Krasikov90
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gravatar for Martin Morgan
6.5 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 02/15/2012 04:44 AM, Vladimir Krasikov wrote: > 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) Install packages using source("http://bioconductor.org/biocLite.R") biocLite("arrayQualityMetrics") this will install the package and all its dependencies (including imports). See also the instructions at http://bioconductor.org/install You might be prompted to update additional packages, which you should do. >> 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 This is an unusual error and it would be good to know if it is repeated when your packages have been installed and updated correctly. If it does still occur, I think you can perhaps provide a bit of debugging information if you say trace(loadNamespace, quote(print(package))) library(arrayQualityMetrics) Martin > 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 > > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 6.5 years ago by Martin Morgan ♦♦ 22k
Thanks Martin It fixes the installation problem Vladimir On Wed, 15 Feb 2012 15:40:09 +0100, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 02/15/2012 04:44 AM, Vladimir Krasikov wrote: >> 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) > > Install packages using > > source("http://bioconductor.org/biocLite.R") > biocLite("arrayQualityMetrics") > > this will install the package and all its dependencies (including > imports). See also the instructions at > > http://bioconductor.org/install > > You might be prompted to update additional packages, which you should do. > >>> 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 > > This is an unusual error and it would be good to know if it is repeated > when your packages have been installed and updated correctly. If it does > still occur, I think you can perhaps provide a bit of debugging > information if you say > > trace(loadNamespace, quote(print(package))) > library(arrayQualityMetrics) > > Martin > >> 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 >> >> >> >> >> > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
ADD REPLYlink written 6.5 years ago by Vladimir Krasikov90
0
gravatar for Wolfgang Huber
6.5 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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? You say "it doesn't work with MAlist objects at all". Can you please provide the exact error message and a reproducible example? 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. 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. 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
ADD COMMENTlink written 6.5 years ago by Wolfgang Huber13k
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 >> >> >> >> >> > > -- Using Opera's revolutionary email client: http://www.opera.com/mail/
ADD REPLYlink written 6.5 years ago by Vladimir Krasikov90
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