BSmooth.tstat error, Error in compute.correction about bsseq HOT 5 OPEN

Hi @yang-mj,

I'm not sure why that it wouldn't be working for the default value of qSd but is for others values both less-than or more-than the default.
It's not a parameter I have much experience with, but perhaps @kasperdanielhansen may be able to provide some ideas.

Cheers,
Pete

from bsseq.

from bsseq.

Hi All,
I am having the same issue while running the tstats. It fails while computing across the sample. I have also tired with estimate.var = "same" but retuned the same error.

@yang-mj, any suggestion whether you were able to fix it?

Thank you,
Priya

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@priyatamapandey I fixed it by swapping these two groups. What I did was only used symmetric CpG sites with minimum 10x coverage (http://smithlabresearch.org/software/methpipe/) and then followed the bsseq pipeline on bsseq's website. So try to set D1 D2 as either group1 or group2 and it'll probably be fixed

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Thank you for your quick reply. I swapped the group as group2 = c("D1","D2") and kept estimate.var = "group2". It did not fail but Is it statistically correct?
As in the base documentation it says that two groups being compared (it is always group1 - group2 ) and estimate.var is considers based on the low variability samples.

I am attaching the plot while looking the plot what cutoff to choose and put in dmrFinder function further, any suggestion is appreciated?

Thank you,
Priya

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