sex chromosome removal steps

[Patrick McGowan]

I have a question regarding the appropriate steps for removing sex chromosomes from analysis. My study design is case/control with equal numbers of males and females in each group.

After running differential methylation analysis using RADmeth, the analysis creates three p values: raw p values, combined p values and FDR. 

I Imported the bed file in R and removed all the sites with negative p values. Then I removed sites on sex chromosomes and re-calculated the FDR using an R function based on the combined p values.

Is this the appropriate method to use?

Alternatively, should I do the alignments, then remove the sex chromosomes (or only keep the autosomal chromosomes), and then get the methylation p-values/FDR values?

Thank you,

Patrick

[Andrew D. Smith]

I think it should be fine, but you might check how it differs if you use the raw p-values instead of combined.

Also, regarding removal of the sex chroms before vs. after doing radmeth, I would try it both ways and see how it differs. The effect of the chrX DMRs/DMPs on overall FDR would depend on the total amount of difference, which in turn depends on the samples you are comparing.

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