Hi all,
I have a question about removing probes from the RG channel set (S4 object) generated by minfi
package. I found the row names for the RG channel set (S4 object) is the probe location IDs on the array instead of probe names started with "cg", so I feel it's not very convenient to filter probes by probe names for this kind of object. Is there a better way to remove or filter probes from this RG channel set (S4 object) by probe names? Thank you so much!
Hi James, thank you for your answer! I am doing the functional normalisation for my EPIC array data, and I think it could be better if I filter out the failed probes (including probes with detection p-values > 0.01, bead count <3, cross-hybridisation, and probes with SNPs) before normalisation. However, I found the input object
RGchannelSet
for thepreprocessFunnorm
function is not easy to subset because the row names are not probe names. Yes,MethylSet
is better thanRGchannelSet
for probe filtering, I think I could probably modifypreprocessFunnorm
a bit to useMethylSet
as input.Hi James, thank you for your answer! I am doing the functional normalisation for my EPIC array data, and I think it could be better if I filter out the failed probes (including probes with detection p-values > 0.01, bead count <3, cross-hybridisation, and probes with SNPs) before normalisation. However, I found the input object
RGchannelSet
for thepreprocessFunnorm
function is not easy to subset because the row names are not probe names. Yes,MethylSet
is better thanRGchannelSet
for probe filtering, I think I could probably modifypreprocessFunnorm
a bit to useMethylSet
as input.There's no need to do any of that. Removing those probes isn't likely to have a material effect on the normalization, so you should probably just use the regular pipeline.
That's very helpful, thank you James!