Something wrong with the running of dmrseq()

[DengEr-1993]

Hello there,

I use dmrseq() with below parameters:

blocks <- dmrseq(bs=bs.filtered, cutoff = 0.1, minNumRegion = 3, ## default 5 smooth = T, testCovariate = "CellType", block = TRUE,

BPPARAM = BiocParallel::bpparam(),

             #BPPARAM = MulticoreParam(workers=6,progressbar=TRUE),
             BPPARAM=bpparam(),##  wrong

             minInSpan = 30,
             bpSpan = 1000,

             maxGapSmooth = 1e6,
             maxGap = 5e4)

But no matter which BPPARAM = I used, the error information always appeared:

Searching for large scale blocks with at least 5000 basepairs. Performing a global test of H0: no difference among 6 groups (assuming the test covariate CellType is a factor). Parallelizing using 6 workers/cores (backend: BiocParallel:MulticoreParam). Computing on 1 chromosome(s) at a time.

Detecting candidate regions with coefficient larger than 0.1 in magnitude. |=============================================================================================================================| 100%

|=========== | 9% Error in (function (cond) : error in evaluating the argument 'args' in selecting a method for function 'do.call': BiocParallel errors 1 remote errors, element index: 118 1225 unevaluated and other errors first remote error: Error in qr.default(t(const)): NA/NaN/Inf in foreign function call (arg 1) In addition: There were 16 warnings (use warnings() to see them)

By the way, the below script works well but it takes a long time.

regions <- dmrseq(bs=bs.filtered, cutoff = 0.1, smooth = T, testCovariate = "CellType", minInSpan = 500, bpSpan = 5e4, maxGapSmooth = 1e6, maxGap = 5e3)

When I set block = TRUE, the step doesn't work.

I tried to add one of below three parameters but the error still exists.

             #BPPARAM = BiocParallel::bpparam(),
             #BPPARAM = MulticoreParam(workers=6,progressbar=TRUE),
             #BPPARAM=bpparam(),##  wrong

So could you give me some advice on this problem ? Thanks a lot.

[kdkorthauer]

Hi,

Thanks for reporting your issue. Could you try to find a small subset of your data that reproduces the same error? If you could send this subset to me as an .rds file here, then I can better diagnose the root cause.

Thank you! Keegan

[DengEr-1993]

Hi,

Thanks for reporting your issue. Could you try to find a small subset of your data that reproduces the same error? If you could send this subset to me as an .rds file here, then I can better diagnose the root cause.

Thank you! Keegan

Thanks for your response. I will double check that. If I cannot solve this question, I will send subset to you.

[DengEr-1993]

Hi,

Thanks for reporting your issue. Could you try to find a small subset of your data that reproduces the same error? If you could send this subset to me as an .rds file here, then I can better diagnose the root cause.

Thank you! Keegan

Hello, it is solved automatically. Maybe it is caused by my computer. Thanks.