Meth27QC: Meth27QC: sample quality analysis, and sample control analysis

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Meth27QC is a tool for analyzing Illumina Infinium HumanMethylation27 BeadChip Data and generating QC reports. This package allows users quickly assess data quality of the Assay. Users can evaluate the data quality in the way that Illumina GenomeStudio/BeadStudio recommended based on the control probes. The package reads files exported from GenomeStudio/BeadStudio software, generating intensity and standard deviation plots grouped by the types of the control probes. Meth27 carries 40 control probes for staining, hybridization, target removal, extension, bisulfite conversion, specificity, negative and non-polymorphic controls. Details of those control probes can be found in the Infinium Assay for Methylation Protocol Guide from Illumina.We also used the other non-control probes to plot intensity of detected genes, signal average for green and red. Outliers can be identified.

Author
Ling Teng, Chao Chen, Chunyu Liu
Date of publication
2011-02-18 07:26:56
Maintainer
Ling Teng <tenglingling@gmail.com>
License
GPL-2
Version
1.1

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Files in this package

Meth27QC
Meth27QC/DESCRIPTION
Meth27QC/inst
Meth27QC/inst/datafile
Meth27QC/inst/datafile/BeadtypeIDs.txt
Meth27QC/inst/DemoData
Meth27QC/inst/DemoData/DEMO_ControlProbeProfile.txt
Meth27QC/inst/DemoData/DEMO_SampleTable.txt
Meth27QC/inst/doc
Meth27QC/inst/doc/Meth27QC_Description.pdf
Meth27QC/man
Meth27QC/man/Meth27QC.rd
Meth27QC/man/QCRep.rd
Meth27QC/NAMESPACE
Meth27QC/R
Meth27QC/R/Meth27QC.r