User: rasmus.rydbirk

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Posts by rasmus.rydbirk

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Comment: C: bumphunter stalls on "Smoothing coefficients"
... I can confirm multi-thread problems: Running with 1 core took 10-25 min for both functions. Thanks! ...
written 5 weeks ago by rasmus.rydbirk10
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Comment: C: bumphunter stalls on "Smoothing coefficients"
... Hi Yuan Thanks for quick reply. I will try overnight with 1 or 4 cores to see if I can get it to work. Can you give me an estimate of running time for this (both DMRs and blocks) when only using one core? Are we talking 10 min/1 h/1 day? /Rasmus Fra: Yuan Tian [bioc] noreply@bioconductor.org Send ...
written 5 weeks ago by rasmus.rydbirk10
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bumphunter stalls on "Smoothing coefficients"
... I've been using bumphunter to get DMR and Blocks as defined in the ChAMP package (champ.DMR and champ.Block functions, respectively) on a MethylationEPIC data set (37 controls, 41 patients). Unfortunately, for both functions, it's stalling at: [bumphunterEngine] Computing coefficients. [bumphunterE ...
bumphunter champ written 5 weeks ago by rasmus.rydbirk10 • updated 5 weeks ago by Yuan Tian90
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Comment: C: Error in champ.load (v. 2.8.3)
... I just tried with ChAMP v. 2.6.x, no problem loading here. My CSV-files look something like this, I of course save them with commas as separators: Sample_Name Real_Name Sample_Group Conversion Sample_Plate Sample_Well Array Slide Basename 1 s1 CTRL ...
written 2.0 years ago by rasmus.rydbirk10
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Error in champ.load (v. 2.8.3)
... I'm not able to import data with champ.load. I don't know if it's a minfi error? > myLoad <- champ.load(arraytype = "EPIC") [===========================] [<<<< ChAMP.LOAD START >>>>>] ----------------------------- [ Loading Data with ChAMP Method ] ---------------- ...
champ written 2.0 years ago by rasmus.rydbirk10 • updated 2.0 years ago by Yuan Tian80
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Comment: C: ChAMP (EPIC): DMRs analysis will not complete
... In my experience, bumphunter takes forever to complete. With 10k+ clusters, I would expect it to take a long (!) time. Can you check CPU usage, is the script still running? You may want to consider looking for a cluster service with more calculating power. If I remember correctly, when I used bumph ...
written 2.2 years ago by rasmus.rydbirk10
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Comment: C: DMRcate fails in ChAMP package
... Hello Yuan Yes, the problem has been resolved, perfect! I'm testing on a Win7x64 machine, I get the error Error in mclapply(chr.unique, fitParallel, object = object, consec = consec,  :    'mc.cores' > 1 is not supported on Windows when I try to run with more than 1 core. However, using only 1 ...
written 2.2 years ago by rasmus.rydbirk10
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Comment: C: champ.impute doesn't update beta matrix
... Wait a minute, you write results to myImpute? Wow.. I feel stupid now. Of course I need to assign a target. I just recieved an output with 0 NAs. Thank you for your help, as always! ...
written 2.3 years ago by rasmus.rydbirk10
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Comment: C: champ.impute doesn't update beta matrix
... Thank you for your reply! My code is: champ.impute(beta=myLoad_Combine$beta, pd=myLoad_Combine$pd, SampleCutoff=0.5) > traceback() 7: cat("Cluster size", p, "broken into", size, "\n") 6: knnimp.split(x, k, imiss, irmiss, p, n, maxp = maxp) 5: knnimp.internal(x[index, ], k, imiss[index, ], irmi ...
written 2.3 years ago by rasmus.rydbirk10
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champ.impute doesn't update beta matrix
... I've been using champ.impute, both Combine and KNN, to replace NAs. After running I receive this (I have 700k+ rows): $beta 1            2            3            4            5            6 5.040964e-03 3.260464e-03 2.506848e-03 6.241857e-03 4.080995e-03 1.144493e-03 1.797270e-01 2.464607e-02 1.09 ...
impute champ bioconductor written 2.3 years ago by rasmus.rydbirk10 • updated 2.3 years ago by Yuan Tian80

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