Question: Illumina Infinium Methylation 450K Demo Data
1
gravatar for ugoodlfy
6.8 years ago by
ugoodlfy30
ugoodlfy30 wrote:

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 .

illumina methylation • 4.6k views
ADD COMMENTlink modified 6.8 years ago by Sean Davis25k • written 6.8 years ago by ugoodlfy30
2
gravatar for Neilfws
6.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Neilfws48k
1
gravatar for Sean Davis
6.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

As of today, it appears that 2215 samples have been assayed on the illumina 450k platform at NCBI GEO.

ADD COMMENTlink written 6.8 years ago by Sean Davis25k

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.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Neilfws48k

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.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Sean Davis25k

That is because the official platform name is Illumina HumanMethylation450 BeadChip. The K would make it not match.

ADD REPLYlink written 6.8 years ago by dario.garvan460

Good search algorithms would account for that and return nearest matches. "HumanMethylation" returns no results, "HumanMethylation450" does. This is just poor search implementation.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Neilfws48k
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