Hi, I am working with TCGA-HNSC methylation data specificallly HNSC-450K. I am interested in finding DMRs with two subgroups (Primary tumor , solid tissue normal). For this purpose i have chosen COHCAP and followed the manual :
https://www.bioconductor.org/packages/release/bioc/manuals/COHCAP/man/COHCAP.pdf
I have made my sample file and data file, still it shows error, there is no valid annotation file. Do i need to prepare files like (GSE42308_truncated.txt, sample_GSE42308.txt, expression_Average_by_Island_truncated.txt, expression-Average-by-Site_truncated.txt).
Also the (platform="450k-UCSC")should be this for my case in case of TCGA -HNSC? as i tried and it didn't work.
I need help with input files format and how to make COHCAP package worked for TCGA-HNSC file. ps: I have downloaded methylation data from firehose gdac.broadinstitute.org_HNSC.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0
