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How to normalize 450K data for cell type composition

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

450k normalization cell type
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updated by igor igor • written by Nicolas Rosewick Nicolas Rosewick

2 answers

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.

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written by andrew.j.skelton73 andrew.j.skelton73

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).

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written by igor igor

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