[BioC] minfi release 1.8

[Elmar Tobi]

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.
>> >
>>
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>
>