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Elmar Tobi
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@elmar-tobi-6246
Last seen 9.7 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.
>
