Hi all,

I have MeDIP-seq data on 4 tumor samples and adjacent normal tissue. In addition, I have INPUT (sequenced non-enriched control same tissue) for each of the sample (8 MEDIPS BAM files and 8 INPUT BAM files). I was wondering whether I can use the INPUT control BAM files in addEnrichmentParameters() rather than using TCGA 450K Human Methylation Calibration Dataset?

I was wondering if anyone has any suggestions as to what R packages or software I can use to produce a similar R object using the INPUT BAM files?

Regards

Gaurav

Hi Gaurav,

the enrichment parameters model the relation between MeDIP enrichment and % methylation, depending on the CpG density. These parameters can be estimated using bisulfite experiments on the same or similar samples (e.g. tcga in the case of cancer) or general assumptions on the relation CpG density and methylation level. Input sequencing does not help here. Note that the calibration is required for the transformation to absolute methylation levels - which is optional. If you just want to compare relative methylation levels between groups of samples calibration is not required.

You can use the input sequencing to estimate CNV levels however.

Best, Matthias