minfi release 1.8
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Elmar Tobi ▴ 30
@elmar-tobi-6246
Last seen 7.7 years ago
Dear Kasper, For older objects I have been trying to update the annotation to IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 But I am getting an error: RGset.c <- updateObject(RGset.7) "Error in if (object at annotation["annotation"] == "ilmn.v1.2") object at annotation["annotation"] <- .default.450k.annotation : missing value where TRUE/FALSE needed" The RGset is a plain one: RGset.7 "RGChannelSet (storageMode: lockedEnvironment) assayData: 622399 features, 605 samples element names: Green, Red phenoData sampleNames: 7310440029_R05C01 7310440029_R05C02 ... 7497398051_R02C01 (605 total) varLabels: hofnum labnr ... v050 (41 total) varMetadata: labelDescription Annotation *array: IlluminaHumanMethylation450k"* (Running on R 3.0.2 with minfi 1.8.8). Do you have any idea on how to update? Best wishes Op woensdag 13 november 2013 01:12:46 UTC+1 schreef Kasper Hansen: > > As part of Bioconductor 2.13, we have released minfi 1.8.x. Due to a > number of last minute errors, the recommended version is 1.8.3 (or bigger). > > Users may find that their old objects cannot be linked to annotation. > Please run > OBJECT = updateObject(OBJECT) > to fix this. > > Highlights include > * preprocessingQuantile(): an independent implementation of the same ideas > as in Tost et al. > * bumphunter() for finding DMRs > * blockFinder() for finding large hypo-methylated blocks on the 450k array. > * estimateCellCounts() for estimating cell type composition for whole > blood samples. The function can be extended to work on other types of > cells, provided suitable flow sorted data is available. > * the annotation now includes SNP annotation for dbSNP v132, 135 and 137, > independently annotated at JHU. > * getSex(): you can now get sex repeatedly, irrespective of relationship > status. > * minfiQC: find and remove outlier samples based on a sample QC criteria > we have found effective. > > Unfortunately, none of these handy changes are yet detailed in the > vignette; we are working on this. > > A manuscript is in review detailing most of these functions. > > Full NEWS below > > Best, > Kasper D Hansen > > o Added getMethSignal(), a convenience function for programming. > > o Changed the argument name of "type" to "what" for getMethSignal(). > > o Added the class "RatioSet", like "GenomicRatioSet" but without the > genome information. > > o Bugfixes to the "GenomicRatioSet()" constructor. > > o Added the method ratioConvert(), for converting a "MethylSet" to a > "RatioSet" or a "GenomicMethylSet" to a "GenomicRatioSet". > > o Fixed an issue with GenomicMethylSet() and GenomicRatioSet() caused > by a recent change to a non-exported function in the GenomicRanges > package (Reported by Gustavo Fernandez Bayon <gba... at="" gmail.com<javascript:=""> > >). > > o Added fixMethOutliers for thresholding extreme observations in the > [un]methylation channels. > > o Added getSex, addSex, plotSex for estimating sex of the samples. > > o Added getQC, addQC, plotQC for a very simple quality control > measure. > > o Added minfiQC for a one-stop function for quality control measures. > > o Changed some verbose=TRUE output in various functions. > > o Added preprocessQuantile. > > o Added bumphunter method for "GenomicRatioSet". > > o Handling signed zero in minfi:::.digestMatrix which caused unit > tests to fail on Windows. > > o addSex and addQC lead to sampleNames() being dropped because of a > likely bug in cbind(DataFrame, DataFrame). Work-around has been > implemented. > > o Re-ran the test data generator. > > o Fixed some Depends and Imports issues revealed by new features of R > CMD check. > > o Added blockFinder and cpgCollapse. > > o (internal) added convenience functions for argument checking. > > o Exposed and re-wrote getAnnotation(). > > o Changed getLocations() from being a method to a simple function. > Arguments have been removed (for example, now the function always > drops non-mapping loci). > > o Implemented getIslandStatus(), getProbeType(), getSnpInfo() and > addSnpInfo(). The two later functions retrieve pre-computed SNP > overlaps, and the new annotation object includes SNPs based on > dbSNP 137, 135 and 132. > > o Changed the IlluminaMethylatioAnnotation class to now include > genomeBuild information as well as defaults. > > o Added estimateCellCounts for deconvolution of cell types in whole > blood. Thanks to Andrew Jaffe and Andres Houseman. >
SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter • 1.6k views
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@kasper-daniel-hansen-2979
Last seen 10 months ago
United States
This should work, but I am unsure why it doesn't. You may have a very old object. Could you send me the output of RGset.7@annotation In the meantime, you should be able to do this by essentially grabbing the slot from minfiData, ie. library(minfiData) data(RGsetEx) RGset.7@annotation = RGsetEx@annotation and then check validObject(RGset.7) (which should return TRUE). Best, Kasper On Mon, Dec 9, 2013 at 10:30 AM, Elmar Tobi <e.tobi@lumc.nl> wrote: > Dear Kasper, > > > For older objects I have been trying to update the annotation to > IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 > But I am getting an error: > > RGset.c <- updateObject(RGset.7) > > "Error in if (object@annotation["annotation"] == "ilmn.v1.2") > object@annotation["annotation"] <- .default.450k.annotation : > missing value where TRUE/FALSE needed" > > > The RGset is a plain one: > > RGset.7 > "RGChannelSet (storageMode: lockedEnvironment) > assayData: 622399 features, 605 samples > element names: Green, Red > phenoData > sampleNames: 7310440029_R05C01 7310440029_R05C02 ... > 7497398051_R02C01 (605 total) > varLabels: hofnum labnr ... v050 (41 total) > varMetadata: labelDescription > Annotation > *array: IlluminaHumanMethylation450k"* > > > (Running on R 3.0.2 with minfi 1.8.8). > > Do you have any idea on how to update? > > Best wishes > > > > > > > Op woensdag 13 november 2013 01:12:46 UTC+1 schreef Kasper Hansen: > > > > As part of Bioconductor 2.13, we have released minfi 1.8.x. Due to a > > number of last minute errors, the recommended version is 1.8.3 (or > bigger). > > > > Users may find that their old objects cannot be linked to annotation. > > Please run > > OBJECT = updateObject(OBJECT) > > to fix this. > > > > Highlights include > > * preprocessingQuantile(): an independent implementation of the same > ideas > > as in Tost et al. > > * bumphunter() for finding DMRs > > * blockFinder() for finding large hypo-methylated blocks on the 450k > array. > > * estimateCellCounts() for estimating cell type composition for whole > > blood samples. The function can be extended to work on other types of > > cells, provided suitable flow sorted data is available. > > * the annotation now includes SNP annotation for dbSNP v132, 135 and 137, > > independently annotated at JHU. > > * getSex(): you can now get sex repeatedly, irrespective of relationship > > status. > > * minfiQC: find and remove outlier samples based on a sample QC criteria > > we have found effective. > > > > Unfortunately, none of these handy changes are yet detailed in the > > vignette; we are working on this. > > > > A manuscript is in review detailing most of these functions. > > > > Full NEWS below > > > > Best, > > Kasper D Hansen > > > > o Added getMethSignal(), a convenience function for programming. > > > > o Changed the argument name of "type" to "what" for > getMethSignal(). > > > > o Added the class "RatioSet", like "GenomicRatioSet" but without > the > > genome information. > > > > o Bugfixes to the "GenomicRatioSet()" constructor. > > > > o Added the method ratioConvert(), for converting a "MethylSet" to > a > > "RatioSet" or a "GenomicMethylSet" to a "GenomicRatioSet". > > > > o Fixed an issue with GenomicMethylSet() and GenomicRatioSet() > caused > > by a recent change to a non-exported function in the > GenomicRanges > > package (Reported by Gustavo Fernandez Bayon <gba...@gmail.com> <javascript:> > > >). > > > > o Added fixMethOutliers for thresholding extreme observations in > the > > [un]methylation channels. > > > > o Added getSex, addSex, plotSex for estimating sex of the samples. > > > > o Added getQC, addQC, plotQC for a very simple quality control > > measure. > > > > o Added minfiQC for a one-stop function for quality control > measures. > > > > o Changed some verbose=TRUE output in various functions. > > > > o Added preprocessQuantile. > > > > o Added bumphunter method for "GenomicRatioSet". > > > > o Handling signed zero in minfi:::.digestMatrix which caused unit > > tests to fail on Windows. > > > > o addSex and addQC lead to sampleNames() being dropped because of a > > likely bug in cbind(DataFrame, DataFrame). Work-around has been > > implemented. > > > > o Re-ran the test data generator. > > > > o Fixed some Depends and Imports issues revealed by new features > of R > > CMD check. > > > > o Added blockFinder and cpgCollapse. > > > > o (internal) added convenience functions for argument checking. > > > > o Exposed and re-wrote getAnnotation(). > > > > o Changed getLocations() from being a method to a simple function. > > Arguments have been removed (for example, now the function always > > drops non-mapping loci). > > > > o Implemented getIslandStatus(), getProbeType(), getSnpInfo() and > > addSnpInfo(). The two later functions retrieve pre- computed SNP > > overlaps, and the new annotation object includes SNPs based on > > dbSNP 137, 135 and 132. > > > > o Changed the IlluminaMethylatioAnnotation class to now include > > genomeBuild information as well as defaults. > > > > o Added estimateCellCounts for deconvolution of cell types in whole > > blood. Thanks to Andrew Jaffe and Andres Houseman. > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Dear Kasper: it returns: "IlluminaHumanMethylation450k" Which is indeed a golden oldie... best, Elmar Op maandag 9 december 2013 16:43:29 UTC+1 schreef Kasper Hansen: > > This should work, but I am unsure why it doesn't. You may have a very old > object. Could you send me the output of > > RGset.7 at annotation > > In the meantime, you should be able to do this by essentially grabbing the > slot from minfiData, ie. > > library(minfiData) > data(RGsetEx) > RGset.7 at annotation = RGsetEx at annotation > > and then check > validObject(RGset.7) > (which should return TRUE). > > Best, > Kasper > > > > > > On Mon, Dec 9, 2013 at 10:30 AM, Elmar Tobi <e.t... at="" lumc.nl="" <javascript:="">>wrote: > >> Dear Kasper, >> >> >> For older objects I have been trying to update the annotation to >> IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 >> But I am getting an error: >> >> RGset.c <- updateObject(RGset.7) >> >> "Error in if (object at annotation["annotation"] == "ilmn.v1.2") >> object at annotation["annotation"] <- .default.450k.annotation : >> missing value where TRUE/FALSE needed" >> >> >> The RGset is a plain one: >> >> RGset.7 >> "RGChannelSet (storageMode: lockedEnvironment) >> assayData: 622399 features, 605 samples >> element names: Green, Red >> phenoData >> sampleNames: 7310440029_R05C01 7310440029_R05C02 ... >> 7497398051_R02C01 (605 total) >> varLabels: hofnum labnr ... v050 (41 total) >> varMetadata: labelDescription >> Annotation >> *array: IlluminaHumanMethylation450k"* >> >> >> (Running on R 3.0.2 with minfi 1.8.8). >> >> Do you have any idea on how to update? >> >> Best wishes >> >> >> >> >> >> >> Op woensdag 13 november 2013 01:12:46 UTC+1 schreef Kasper Hansen: >> > >> > As part of Bioconductor 2.13, we have released minfi 1.8.x. Due to a >> > number of last minute errors, the recommended version is 1.8.3 (or >> bigger). >> > >> > Users may find that their old objects cannot be linked to annotation. >> > Please run >> > OBJECT = updateObject(OBJECT) >> > to fix this. >> > >> > Highlights include >> > * preprocessingQuantile(): an independent implementation of the same >> ideas >> > as in Tost et al. >> > * bumphunter() for finding DMRs >> > * blockFinder() for finding large hypo-methylated blocks on the 450k >> array. >> > * estimateCellCounts() for estimating cell type composition for whole >> > blood samples. The function can be extended to work on other types of >> > cells, provided suitable flow sorted data is available. >> > * the annotation now includes SNP annotation for dbSNP v132, 135 and >> 137, >> > independently annotated at JHU. >> > * getSex(): you can now get sex repeatedly, irrespective of relationship >> > status. >> > * minfiQC: find and remove outlier samples based on a sample QC criteria >> > we have found effective. >> > >> > Unfortunately, none of these handy changes are yet detailed in the >> > vignette; we are working on this. >> > >> > A manuscript is in review detailing most of these functions. >> > >> > Full NEWS below >> > >> > Best, >> > Kasper D Hansen >> > >> > o Added getMethSignal(), a convenience function for programming. >> > >> > o Changed the argument name of "type" to "what" for >> getMethSignal(). >> > >> > o Added the class "RatioSet", like "GenomicRatioSet" but without >> the >> > genome information. >> > >> > o Bugfixes to the "GenomicRatioSet()" constructor. >> > >> > o Added the method ratioConvert(), for converting a "MethylSet" >> to a >> > "RatioSet" or a "GenomicMethylSet" to a "GenomicRatioSet". >> > >> > o Fixed an issue with GenomicMethylSet() and GenomicRatioSet() >> caused >> > by a recent change to a non-exported function in the >> GenomicRanges >> > package (Reported by Gustavo Fernandez Bayon <gba... at="" gmail.com="">> <javascript:> >> > >). >> > >> > o Added fixMethOutliers for thresholding extreme observations in >> the >> > [un]methylation channels. >> > >> > o Added getSex, addSex, plotSex for estimating sex of the samples. >> > >> > o Added getQC, addQC, plotQC for a very simple quality control >> > measure. >> > >> > o Added minfiQC for a one-stop function for quality control >> measures. >> > >> > o Changed some verbose=TRUE output in various functions. >> > >> > o Added preprocessQuantile. >> > >> > o Added bumphunter method for "GenomicRatioSet". >> > >> > o Handling signed zero in minfi:::.digestMatrix which caused unit >> > tests to fail on Windows. >> > >> > o addSex and addQC lead to sampleNames() being dropped because of >> a >> > likely bug in cbind(DataFrame, DataFrame). Work-around has been >> > implemented. >> > >> > o Re-ran the test data generator. >> > >> > o Fixed some Depends and Imports issues revealed by new features >> of R >> > CMD check. >> > >> > o Added blockFinder and cpgCollapse. >> > >> > o (internal) added convenience functions for argument checking. >> > >> > o Exposed and re-wrote getAnnotation(). >> > >> > o Changed getLocations() from being a method to a simple function. >> > Arguments have been removed (for example, now the function >> always >> > drops non-mapping loci). >> > >> > o Implemented getIslandStatus(), getProbeType(), getSnpInfo() and >> > addSnpInfo(). The two later functions retrieve pre- computed SNP >> > overlaps, and the new annotation object includes SNPs based on >> > dbSNP 137, 135 and 132. >> > >> > o Changed the IlluminaMethylatioAnnotation class to now include >> > genomeBuild information as well as defaults. >> > >> > o Added estimateCellCounts for deconvolution of cell types in >> whole >> > blood. Thanks to Andrew Jaffe and Andres Houseman. >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Biocon... at r-project.org <javascript:> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >
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