Hello guys, I need some illumina Infinium Methylation 450K demo data to play. I have search online for a long time , but can only find some tools like IMA(Illumina Methylation Analyzer) and methylumi etc. Is anybody know some databases provide illumina Infinium Methylation 450K demo data ? Thanks a lot .
There is publicly-available 450K data in The Cancer Genome Atlas (TCGA).
It's a little difficult to navigate for new users. I would start with the data matrix and select, for example COAD (colon adenocarcinoma), then DNA Methylation under Data Type. You should then see JHU_USC HumanMethylation450 under Center/Platform.
There's also direct FTP access; here's the COAD 450K directory.
You'll need to spend some time reading the TCGA documentation to figure out their barcode system.
As of today, it appears that 2215 samples have been assayed on the illumina 450k platform at NCBI GEO.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Incredible: I ran a search of platforms there yesterday using "450K" as query, nothing came up. Today, search will not even complete (returns an error). Search/retrieval at GEO is just appalling.
Do report your problems to <geo at="" ncbi.nlm.nih.gov="">. They have typically been responsive when I have found errors and other major problems.
That is because the official platform name is Illumina HumanMethylation450 BeadChip. The K would make it not match.
Good search algorithms would account for that and return nearest matches. "HumanMethylation" returns no results, "HumanMethylation450" does. This is just poor search implementation.