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.

Functions for analysis of method comparison studies.
Bendix Carstensen, Lyle Gurrin, Claus Ekstrom
R2WinBUGS, coda, BRugs, lattice, rjags, lme4
Methods (standard and advanced) for comparison of
measurement methods.

Functions for Analysis of Agreement in Method Comparison Studies
Bendix Carstensen, Lyle Gurrin, Claus Ekstrom, Michal Figurski
R2WinBUGS, BRugs, rjags, coda, lattice, lme4
Methods (standard and advanced) for analysis of agreement
between measurement methods.

Functions for analysis of agreement in method comparison
studies.

Analysis of Agreement in Method Comparison Studies
c(person(given="Bendix", family="Carstensen", email="b@bxc.dk", role=c("aut")),
person(given="Lyle", family="Gurrin", email="lgurrin@unimelb.edu.au", role=c("aut")),
person(given="Claus Thorn", family="Ekstrøm", email="ekstrom@sund.ku.dk", role=c("aut", "cre")),
person(given="Michal", family="Figurski", email="figurski@mail.med.upenn.edu", role=c("aut")))
Methods (standard and advanced) for analysis of agreement between measurement methods. These cover Bland-Altman plots, Deming regression, Lin's Total deviation index, and difference-on-average regression. See Carstensen B. (2010) "Comparing Clinical Measurement Methods: A Practical Guide (Statistics in Practice)" <doi:10.1002/9780470683019> for more information.
Bendix Carstensen [aut],
Lyle Gurrin [aut],
Claus Thorn Ekstrøm [aut, cre],
Michal Figurski [aut]