arrayQualityMetrics error with MAList
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karen power ▴ 10
@karen-power-5140
Last seen 9.7 years ago
Hi, I'm trying to use arrayQualityMetrics to investigate 2 colour Agilent microarrays. However I get the following error; > arrayQualityMetrics(MA.avg_TEST1, outdir="Test1_report") The report will be written into directory 'Test1_report'. 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. I have no idea how to succesfully turn an MAList into NChannelSet as "MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet')" doesn't work. Is it something I'm doing wrong with the arrayQualityMetrics command? Or else is there a way around it? Session is as follows; > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_3.10.0 BiocInstaller_1.2.1 limma_3.10.2 loaded via a namespace (and not attached): [1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.1 AnnotationDbi_1.16.18 beadarray_2.4.1 Biobase_2.14.0 Biostrings_2.22.0 [9] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5 genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6 [17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0 RColorBrewer_1.0-5 RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.2 survival_2.36-12 [25] SVGAnnotation_0.9-0 tools_2.14.2 vsn_3.22.0 XML_3.9-4 xtable_1.7-0 zlibbioc_1.0.0 Regards, Karen Karen Power BSc PhD Room 039, UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland. [[alternative HTML version deleted]]
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@wolfgang-huber-3550
Last seen 28 days ago
EMBL European Molecular Biology Laborat…
Dear Karen what happens when you run library("convert") before MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet') If that does not help, can you please send me (offline) the offending object 'MA.avg_TEST1'? I suspect I need to fix the NAMESPACE of arrayQualiyMetrics, sorry for that. best wishes Wolfgang Mar/1/12 3:45 PM, karen power scripsit:: > Hi, > > I'm trying to use arrayQualityMetrics to investigate 2 colour Agilent > microarrays. However I get the following error; > >> arrayQualityMetrics(MA.avg_TEST1, outdir="Test1_report") > The report will be written into directory 'Test1_report'. > 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. > > > I have no idea how to succesfully turn an MAList into NChannelSet as > "MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet')" > doesn't work. > > Is it something I'm doing wrong with the arrayQualityMetrics command? Or else is > there a way around it? Session is as follows; > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] arrayQualityMetrics_3.10.0 BiocInstaller_1.2.1 limma_3.10.2 > > loaded via a namespace (and not attached): > [1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0 > annotate_1.32.1 AnnotationDbi_1.16.18 beadarray_2.4.1 Biobase_2.14.0 > Biostrings_2.22.0 > [9] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5 > genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 > IRanges_1.12.6 > [17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0 > RColorBrewer_1.0-5 RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.2 > survival_2.36-12 > [25] SVGAnnotation_0.9-0 tools_2.14.2 vsn_3.22.0 XML_3.9-4 > xtable_1.7-0 zlibbioc_1.0.0 > > > > Regards, > > Karen > > Karen Power BSc PhD > Room 039, > UCD Centre for Food Safety, > School of Public Health, Physiotherapy and Population Science > Veterinary Sciences Centre, > University College Dublin, > Belfield, > Dublin 4, > Ireland. > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Karen in fact, there is no coercion method from MAList to NChannelSet, yet there is one from MAList to ExpressionSet (and all that actually makes sense). Thus, can you please try library(convert) MA.avg_TEST1_eSet <- as(MA.avg_TEST1, 'ExpressionSet') arrayQualityMetrics(MA.avg_TEST1_eSet, outdir="Test1_report") Let me know if that works. Sometimes it happens that this fails with an error, since the metadata in limma MALists tends to be less strictly organised than what is expected by Biobase. In that case, send me the offending object, and I will try to tweak the coercion method to deal with it. Best wishes Wolfgang Mar/1/12 9:48 PM, Wolfgang Huber scripsit:: > Dear Karen > > what happens when you run > > library("convert") > > before > > MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet') > > If that does not help, can you please send me (offline) the offending > object 'MA.avg_TEST1'? > > I suspect I need to fix the NAMESPACE of arrayQualiyMetrics, sorry for > that. > > best wishes > Wolfgang > > Mar/1/12 3:45 PM, karen power scripsit:: >> Hi, >> >> I'm trying to use arrayQualityMetrics to investigate 2 colour Agilent >> microarrays. However I get the following error; >> >>> arrayQualityMetrics(MA.avg_TEST1, outdir="Test1_report") >> The report will be written into directory 'Test1_report'. >> 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. >> >> >> I have no idea how to succesfully turn an MAList into NChannelSet as >> "MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet')" >> doesn't work. >> >> Is it something I'm doing wrong with the arrayQualityMetrics command? >> Or else is >> there a way around it? Session is as follows; >> >>> sessionInfo() >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] arrayQualityMetrics_3.10.0 BiocInstaller_1.2.1 limma_3.10.2 >> >> loaded via a namespace (and not attached): >> [1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0 >> annotate_1.32.1 AnnotationDbi_1.16.18 beadarray_2.4.1 Biobase_2.14.0 >> Biostrings_2.22.0 >> [9] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5 >> genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 >> IRanges_1.12.6 >> [17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0 >> RColorBrewer_1.0-5 RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.2 >> survival_2.36-12 >> [25] SVGAnnotation_0.9-0 tools_2.14.2 vsn_3.22.0 XML_3.9-4 >> xtable_1.7-0 zlibbioc_1.0.0 >> >> >> >> Regards, >> >> Karen >> >> Karen Power BSc PhD >> Room 039, >> UCD Centre for Food Safety, >> School of Public Health, Physiotherapy and Population Science >> Veterinary Sciences Centre, >> University College Dublin, >> Belfield, >> Dublin 4, >> Ireland. >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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@wolfgang-huber-3550
Last seen 28 days ago
EMBL European Molecular Biology Laborat…
Dear Karen I have just put a method into arrayQualityMetrics for 'MAList' objects. Version 3.11.3 should come into the devel branch within 1-2 days: http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetri cs.html I'm not doing much two-colour microarray analysis these days, so I will be interested in your experience with it, and further suggestions. Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, I just tested arrayQualityMetrics 3.11.4 on 'MAList' objects and it is working for me (it generates a report). However, I am not sure I understand what is going on. From the box plot and density plot it looks like it is using data that are not log transformed as some expression values are very large. Surprisingly, it makes no difference whether I set 'do.logtransform=FALSE' or 'do.logtransform=TRUE'. The plots are identical and looks as if they are made on non-log- transformed data. I also tried to convert the data manually, as you suggested: eset <- as(MA, 'ExpressionSet'). However, this yielded expression values from -9 to 13 and did not work: > min(exprs(eset)) [1] -9.230704 > max(exprs(eset)) [1] 13.12851 Another question: is there a way to make arrayQualityMetrics create MA-plots and spatial plots for all arrays and not just a subset? I think that would be a nice feature, but I could not find it. For example, it would make it easier to compare MA-plots before and after normalization. As it is now, it may plot MA-plots for different arrays before and after normalization. Best, Daniel On Mar 4, 2012, at 9:00 PM, Wolfgang Huber wrote: > Dear Karen > > I have just put a method into arrayQualityMetrics for 'MAList' objects. > > Version 3.11.3 should come into the devel branch within 1-2 days: ht tp://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics .html > > I'm not doing much two-colour microarray analysis these days, so I will be interested in your experience with it, and further suggestions. > > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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
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Dear Daniel thank you for pointing out this problem. In version 3.11.4, the values for the red and green channels were computed by exponentiating (base 2) the values R = A+M/2 and G = A-M/2. From version, 3.11.5 (in subversion, should be on the web in a few days), no exponentiating is done. I hope you will find that behaviour more pleasing. If questions persist, please send me your example dataset and script. More below. Mar/9/12 12:33 PM, Daniel Aaen Hansen scripsit:: > Dear Wolfgang, > > I just tested arrayQualityMetrics 3.11.4 on 'MAList' objects and it > is working for me (it generates a report). However, I am not sure I > understand what is going on. From the box plot and density plot it > looks like it is using data that are not log transformed as some > expression values are very large. Surprisingly, it makes no > difference whether I set 'do.logtransform=FALSE' or > 'do.logtransform=TRUE'. The plots are identical and looks as if they > are made on non-log-transformed data. > > I also tried to convert the data manually, as you suggested: eset<- > as(MA, 'ExpressionSet'). However, this yielded expression values from > -9 to 13 and did not work: Yes, this creates an ExpressionSet from the M values only. The value range you quote seems consistent with that. However, doing that conversion is much inferior to the current functionality for MAList in arrayQualityMetrics, so please ignore that previous suggestion. >> min(exprs(eset)) > [1] -9.230704 >> max(exprs(eset)) > [1] 13.12851 > > Another question: is there a way to make arrayQualityMetrics create > MA-plots and spatial plots for all arrays and not just a subset? I > think that would be a nice feature, but I could not find it. For > example, it would make it easier to compare MA-plots before and after > normalization. As it is now, it may plot MA-plots for different > arrays before and after normalization. Currently, it is not that easy, but of course, this being R and open source, it is possible. You need to create your own version of the function 'aqm.maplot', and e.g. replace the line if (x$numArrays <= 8) { by if (TRUE) { Then you also need to make sure that the function 'arrayQualityMetrics' finds your version of 'aqm.maplot'. This is done either by putting the latter back into the namespace of the package 'arrayQualityMetrics', or by also creating your own version of the function 'arrayQualityMetrics' (which is quite short and simple, it just successively calls the functions creating the various report parts.) See also the vignette "Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output". If someone comes up with a user-interface that allows exposing this (and similar) options to the user at the level of the 'arrayQualityMetrics' function without creating a plethora of parameter options, I will implement it in the package. (The 'philosophy' of the package is to produce a reasonable report for almost everyone with default settings; whereas customisations can be obtained through using the flexibility of the R language, and a modular design of the package functionality - rather than banging in lots and lots of parameters and options into a monolithic function.) Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, The plots are definitely more useful now. Thanks. Regarding implementing an option for plotting all MA-plots and spatial plots, I would suggest a user option 'plot.all' which are false by default to mimic the current behavior. Then in the functions 'aqm.maplot' and 'spatialplot', I suggest adding: if (plot.all) { whj = order(stat, decreasing = TRUE) lay = c(4, ceiling(x$numArrays/4)) legOrder = "" } else if (x$numArrays <= 8) { ... (default behavior) Thus, if plot.all is set to true, all arrays are plottet and if not, it will behave as it does now. I still think it's useful to order plots by the statistic and I also changed the layout to always be 4 columns. This is only relevant to the MA-plots and spatial plots since for the other plots, all arrays are already included in the plots. Best, Daniel On Mar 15, 2012, at 11:17 PM, Wolfgang Huber wrote: > Dear Daniel > > thank you for pointing out this problem. In version 3.11.4, the > values for the red and green channels were computed by > exponentiating (base 2) the values R = A+M/2 and G = A-M/2. From > version, 3.11.5 (in subversion, should be on the web in a few days), > no exponentiating is done. I hope you will find that behaviour more > pleasing. > > If questions persist, please send me your example dataset and > script. More below. > > Mar/9/12 12:33 PM, Daniel Aaen Hansen scripsit:: >> Dear Wolfgang, >> >> I just tested arrayQualityMetrics 3.11.4 on 'MAList' objects and it >> is working for me (it generates a report). However, I am not sure I >> understand what is going on. From the box plot and density plot it >> looks like it is using data that are not log transformed as some >> expression values are very large. Surprisingly, it makes no >> difference whether I set 'do.logtransform=FALSE' or >> 'do.logtransform=TRUE'. The plots are identical and looks as if they >> are made on non-log-transformed data. >> >> I also tried to convert the data manually, as you suggested: eset<- >> as(MA, 'ExpressionSet'). However, this yielded expression values from >> -9 to 13 and did not work: > > Yes, this creates an ExpressionSet from the M values only. The value > range you quote seems consistent with that. However, doing that > conversion is much inferior to the current functionality for MAList > in arrayQualityMetrics, so please ignore that previous suggestion. > >>> min(exprs(eset)) >> [1] -9.230704 >>> max(exprs(eset)) >> [1] 13.12851 >> >> Another question: is there a way to make arrayQualityMetrics create >> MA-plots and spatial plots for all arrays and not just a subset? I >> think that would be a nice feature, but I could not find it. For >> example, it would make it easier to compare MA-plots before and after >> normalization. As it is now, it may plot MA-plots for different >> arrays before and after normalization. > > Currently, it is not that easy, but of course, this being R and open > source, it is possible. You need to create your own version of the > function 'aqm.maplot', and e.g. replace the line > if (x$numArrays <= 8) { > by > if (TRUE) { > > Then you also need to make sure that the function > 'arrayQualityMetrics' finds your version of 'aqm.maplot'. This is > done either by putting the latter back into the namespace of the > package 'arrayQualityMetrics', or by also creating your own version > of the function 'arrayQualityMetrics' (which is quite short and > simple, it just successively calls the functions creating the > various report parts.) > > See also the vignette "Advanced topics: Customizing > arrayQualityMetrics reports and programmatic processing of the > output". > > If someone comes up with a user-interface that allows exposing this > (and similar) options to the user at the level of the > 'arrayQualityMetrics' function without creating a plethora of > parameter options, I will implement it in the package. > > (The 'philosophy' of the package is to produce a reasonable report > for almost everyone with default settings; whereas customisations > can be obtained through using the flexibility of the R language, and > a modular design of the package functionality - rather than banging > in lots and lots of parameters and options into a monolithic > function.) > > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > >
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