Question: Copy number analysis from Illumina 550K chip
0
gravatar for stuti.agrawal
4.1 years ago by
United States
stuti.agrawal0 wrote:

Hi,

I am trying to use CRLMM for copy number analysis and genotyping of some human cancer samples on a Illumina 550K SNP chip. Can I used the CRLMM package for this purpose and if so, which is the annotation package I should be using? 

I only have the .idat files for these samples and no samplesheets.

Thanks,

Stuti Agrawal

crlmm copynumber illumina • 949 views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by stuti.agrawal0
Answer: Copy number analysis from Illumina 550K chip
0
gravatar for andrew.j.skelton73
4.1 years ago by
United Kingdom
andrew.j.skelton73320 wrote:

I'm not sure why you really want to do copy number analysis on methylation data, nonetheless there is a package made for that: Conumee

CRLMM is designed for Genotyping chips, whereas you have Methylation Chips. 

ADD COMMENTlink written 4.1 years ago by andrew.j.skelton73320

Also, I think you mean 450K, not 550K

ADD REPLYlink written 4.1 years ago by andrew.j.skelton73320
Answer: Copy number analysis from Illumina 550K chip
0
gravatar for stuti.agrawal
4.1 years ago by
United States
stuti.agrawal0 wrote:

Hi Andrew,

Thank you for your response. I am trying to do an analysis on the copy number data from the TARGET project (https://target.nci.nih.gov/dataMatrix/). The Neuroblastoma (NBL) project has copy number data on an Illumina 550K chip and I am trying to do an analysis on that. However, these idat files are controlled access and I cannot share them. 

This is not methylation data, I only tried to use that because I wanted to get a hang of CRLMM using some public data so that I can share results if I face problems. However, I now realize that I was testing on a dataset that is not close to my actual dataset.

Could you please provide me some guidance on how to use CRLMM for these NBL datasets, such as which cdf to use?

Thank you,

Stuti

ADD COMMENTlink written 4.1 years ago by stuti.agrawal0
1

Oh, so these are HumanHap550-Quad+ BeadChips? If that's the case, I think this is the one you're looking for. 

ADD REPLYlink written 4.1 years ago by andrew.j.skelton73320
Answer: Copy number analysis from Illumina 550K chip
0
gravatar for stuti.agrawal
4.1 years ago by
United States
stuti.agrawal0 wrote:

Hi Andrew, 

Thank you very much for your quick response.

Do you know of any public datasets of iDAT files which are on the 550K chip?

Thanks,

Stuti

ADD COMMENTlink written 4.1 years ago by stuti.agrawal0

GEO is probably your best bet, but I'm not hugely familiar with SNP Chips. 

ADD REPLYlink written 4.1 years ago by andrew.j.skelton73320
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