2.9 years ago by

Cambridge, United Kingdom

I haven't worked with methylation data, but from what I understand, you should be applying *limma* on M-values. These are more accurately modelled under normality, at least in regard to the range of values, the mean-variance relationship, etc. Some people seem to do all the linear modelling with M-values, and then report back the fold-changes, etc. for significant probes in terms of beta-values, which are easier to interpret.

Anyway, the `logFC`

field should represent the change in the average M-value between conditions, which - I think - is interpretable as a change in the log-odds of methylation. For example, a `logFC`

of 1 would indicate that in one condition, the odds of being methylated to being nonmethylated are twice as high as the other condition. Or, in the simplest terms: larger `logFC`

= stronger differential methylation. The `AveExpr`

field would be the average M-value across all samples, which gives you a measure of the overall amount of methylation for each probe. The B-statistic is the log-odds of differential methylation to constant methylation (note, *not* the log-odds of methylation to nonmethylation, which is the M-value itself). I tend not to use the B-statistic much for DE analyses as I find it a bit unintuitive, but to each his own.

Finally, the chosen reference depends on the parametrization of the design matrix. If you have a one-way layout and you construct a design with an intercept via `model.matrix`

, the alphabetically-first group will be the reference.

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modified 2.9 years ago
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2.9 years ago by
Aaron Lun • **21k**