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

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.

Install the latest version of this package by entering the following in R:
install.packages("Meth27QC")
AuthorLing Teng, Chao Chen, Chunyu Liu
Date of publication2011-02-18 07:26:56
MaintainerLing Teng <tenglingling@gmail.com>
LicenseGPL-2
Version1.1

View on CRAN

Functions

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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