This tool calculate the DNA methylation age
using the Skin Specific Molecular Clock
Pre-processed (beta values) measured on the Illumina BeadChip platform.
How to use
To run the algorithm, the input file must be in a matrix format containing beta values, representing methylation levels of each probe (rows) for each sample (columns). The matrix must contain beta values, ideally obtained using the R package "minfi".
The package minfi User's Guide provides instructions for how to obtain beta values from the raw .idat files. Beta values should be normalized using the betaqn() method, which quantile normalizes betas, implemented by the "wateRmelon"package.
This step is not mandatory, but enhances results' accuracy.
In order to accurately predict the DNAm ages, the final matrix must contain information about all features (probes). Sometimes, due to scanning or hybridization problems, the information about some probes will be unavailable, leading to errors. In case your data have missing probes, try to use inputations methods to fill this gap. If there are no missing probes, just upload your dataset.
When the process finishes, you will receive the result by email.
The dataset is composed of 16 skin biopsy samples from female donors, age 29-60. All data was generated using the Illumina Infinium HumanMethylation850 BeadChip (GEO accession number GSE151600).
Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging - Mariana Boroni*, Alessandra Zonari; Carolina Reis de Oliveira; Kallie Alkatib; Edgar Cruz; Lear E Brace; Juliana Lott de Carvalho.
*Corresponding author. Email: [email protected]. Phone: +55 21 32076550 Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.