I'm interested in getting an M value for each cpg from an Illumina 450k array, but the data was deposited in unmethylated and methylated signal in this GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53840), is there a simple method to create the M values from this matrix, or would I have to manually input the equation into R and do sapply? In which case, it would be
log2((methylated +1)/(unmethylated+1)) from pan du et al. 2016? Thanks for helping a noob out!
ID_REF SAMPLE1 Unmethylated Signal SAMPLE1 Methylated Signal cg00035864 4327 863 cg00050873 640 11173 cg00061679 981 2215 cg00063477 299 4303 cg00121626 3382 6491 cg00212031 3721 405 cg00213748 391 1558 cg00214611 4018 219 cg00223952 7333 584 cg00243321 5591 13