@@ -3,7 +3,7 @@ Quality control, probe/sample filtering and normalization of Infinium HumanMethy
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@@ -3,7 +3,7 @@ Quality control, probe/sample filtering and normalization of Infinium HumanMethy
Maarten van Iterson, Elmar Tobi, Roderick Slieker, Wouter den Hollander, Koen Dekkers, Rene Luijk, Eline Slagboom and Bas Heijmans Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
Maarten van Iterson, Elmar Tobi, Roderick Slieker, Wouter den Hollander, Koen Dekkers, Rene Luijk, Eline Slagboom and Bas Heijmans Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
20 September 2016
20 September 2016
A nice rendered document is available from [here](http://bios-vm.bbmrirp3-lumc.vm.surfsara.nl/BIOSRutils/Leiden450K.html)!
A nicely rendered document is available from [here](http://bios-vm.bbmrirp3-lumc.vm.surfsara.nl/BIOSRutils/Leiden450K.html)!
Introduction
Introduction
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@@ -12,7 +12,7 @@ Here we provide a complete workflow for the the preprocessing and analysis of DN
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@@ -12,7 +12,7 @@ Here we provide a complete workflow for the the preprocessing and analysis of DN
The *Leiden450K*-package contains a series of convenient functions for the quality control, normalization and analysis of methylation array data. The workflow has been thoroughly tested on 450k array data but will similarly be applicable to the newer 850k EPIC array pending updates of Bioconductor packages from other groups.
The *Leiden450K*-package contains a series of convenient functions for the quality control, normalization and analysis of methylation array data. The workflow has been thoroughly tested on 450k array data but will similarly be applicable to the newer 850k EPIC array pending updates of Bioconductor packages from other groups.
The workflow and package extensively uses functionality of other BioConductor packages, e.g., for transforming idats to so-called `RGlist` we use *[minfi](http://bioconductor.org/packages/release/bioc/html/minfi.html)* but *Leiden450K* provides functionality to do this in parallel. Furthermore, we have developed two other packages *[MethylAid](http://bioconductor.org/packages/release/bioc/html/MethylAid.html)*(M. van Iterson et al. 2014) and *[bacon](http://bioconductor.org/packages/release/bioc/html/bacon.html)*(M. M. van Iterson et al. 2016), reps., performing interactive sample quality control and bias- and inflation-correction in epigenomewide association studies, each have been deposited at BioConductor (of note: *[bacon](http://bioconductor.org/packages/release/bioc/html/bacon.html)* also applies to transcriptome- and any other ome-wide association studies) .
The workflow and package extensively uses functionality of other BioConductor packages, e.g., for transforming idats to so-called `RGlist` we use *[minfi](http://bioconductor.org/packages/release/bioc/html/minfi.html)* but *Leiden450K* provides functionality to do this in parallel. Furthermore, we have developed two other packages *[MethylAid](http://bioconductor.org/packages/release/bioc/html/MethylAid.html)*(M. van Iterson et al. 2014) and *[bacon](http://bioconductor.org/packages/release/bioc/html/bacon.html)*(M. van Iterson et al. 2016), reps., performing interactive sample quality control and bias- and inflation-correction in epigenomewide association studies, each have been deposited at BioConductor (of note: *[bacon](http://bioconductor.org/packages/release/bioc/html/bacon.html)* also applies to transcriptome- and any other ome-wide association studies) .