Matthew Suderman

Sorry about the silence on this. Thank you for pointing out this problem. I might realistically be able to have a look at this in more detail in May. It...

Sorry to hear about this error. Could you run the following code and send me the output generated? ```r outlier.sd

Ah I see. The qc.summary() is failing when it attempts to identify outliers because only one sample is being analysed. Although some quality information can be generated for a single...

and this Park, Y., Figueroa, M. E., Rozek, L. S., & Sartor, M. A. (2014). MethylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics (Oxford, England), 30(17), 2414–2422. https://doi.org/10.1093/bioinformatics/btu339

The function is attempting to identify the most likely beadchip (e.g. 450k, epic or epic2). This isn't working as expected because Illumina keeps making small changes to the exact CpG...

This set of sites is a bit unusual for two reasons: 1. It includes 6 CpG sites (cg08004823, cg09485900, cg11311583, cg16439470, cg20048544, cg22746433) that I've not seen before. It's possible...

I've added a new function, meffil.autosomal.subset(). It will identify the autosomal sites among a set of Illumina CpG site names. In your code, you could use it like this: autosomal.sites

This is due to a typo in a recent change I made. Just fixed this yesterday, so you should just be able to reinstall from github. ________________________________ From: Lidija0710 ***@***.***>...

Hi Rafael, Sorry to hear that. NA values are due to probe values being identified as unreliable during the QC step, so the QC report would give some idea why...

Hi Mao, With just the error message, I can only guess. It's possible that you have encountered this error: https://support.bioconductor.org/p/122925/ If so, then reinstalling preprocessCore as follows should fix the...