Ovarian cancer DNA methylation dataset (level 1 data: raw) together with clinical files was downloaded from TCGA in January 2001 (method: create an archive, use wget to download the archive). It is stored on belltown:
/work/DAT_002__TCGA_Ovarian/01_2011
Total number of patients is 520. DNA methylation platform: Illumina HumanMethylation27k, composed of ~27k CpGs.
The raw data for each patient is represented in a single file. First row (Hybridization REF, patient ID...), second row: Composite Element REF (Illumina's CpG ID), Methylated_Signal_Intensity (M), M_Number_Beads, M_STDERR, Un-Methylated_Signal_Intensity (U), U_Number_Beads, U_STDERR, Negative_Control_Grn_Avg_Intensity, Negative_Control_Grn_STDERR, Negative_Control_Red_Avg_Intensity, Negative_Control_Red_STDERR, Detection_P_Value.
To be added: general info about the platform, available methods for calculating methylated status.