Question: How to normalize 450K data for cell type composition
1
gravatar for Nicolas Rosewick
3.7 years ago by
Belgium, Brussels
Nicolas Rosewick8.6k wrote:

Hi,

I've a bunch of 450K (Infinium HumanMethylation450 BeadChip) methylation data from leukemic cells. I read that cell type composition (CD8, CD4, NK, ...) could biais the analysis. I was able to compute the cell composition using the estimateCellCounts function from minfi package. But now how can I normalize my beta (and M) values using these informations ?

Thanks you

cell type normalization 450k • 1.7k views
ADD COMMENTlink modified 2.7 years ago by igor9.6k • written 3.7 years ago by Nicolas Rosewick8.6k
1
gravatar for andrew.j.skelton73
3.7 years ago by
London
andrew.j.skelton735.9k wrote:

See this post - Kasper Hansen replied to a similar question I wrote about this (admittedly it was about a year ago), and stated that although the estimateCellCounts function can identify biases, it isn't clear what the best way to adjust for this is.

ADD COMMENTlink written 3.7 years ago by andrew.j.skelton735.9k
1
gravatar for igor
2.7 years ago by
igor9.6k
United States
igor9.6k wrote:

This is very delayed, but it seems there is another package celltypes450 that can adjust beta values for cell-type composition: https://github.com/brentp/celltypes450

It was originally created before estimateCellCounts was available. Perhaps there is a good reason why estimateCellCounts doesn't offer such functionality (see andrew.j.skelton73's answer).

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by igor9.6k
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