User: rasmus.rydbirk

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Posts by rasmus.rydbirk

<prev • 14 results • page 1 of 2 • next >
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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 5 months 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 5 months ago by rasmus.rydbirk10 • updated 5 months ago by Yuan Tian70
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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 7 months 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 7 months 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 8 months 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 8 months 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): $beta 1            2            3            4            5            6 5.040964e-03 3.260464e-03 2.506848e-03 6.241857e-03 4.080995e-03 1.144493e-03 1.797270e-01 2.464607e-02 1.09 ...
impute champ bioconductor written 8 months ago by rasmus.rydbirk10 • updated 8 months ago by Yuan Tian70
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Comment: C: Error in champ.CNA (v. 2.6.0)
... Additional information: BiocInstaller::biocValid() is OK. traceback(): 1: champ.CNA(intensity = myLoad$intensity, controlGroup = "CTRL",         sampleCNA = FALSE, groupFreqPlots = TRUE, Rplot = FALSE,         arraytype = "EPIC") sessionInfo(): R version 3.3.3 (2017-03-06) Platform: x86_64-w64- ...
written 8 months ago by rasmus.rydbirk10
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Comment: C: Manhattan plot from ChAMP data
... Thank you for the reply. As I understand it, Manhattan plots can be made using beta value ranges (example: http://dx.doi.org/10.1007/s12017-014-8332-8) or simply -log10(p) (https://en.wikipedia.org/wiki/Manhattan_plot). Beta values are already available after champ.impute (or before if impute is no ...
written 8 months ago by rasmus.rydbirk10
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Comment: C: DMRcate fails in ChAMP package
... Thank you for the quick reply! I was assuming something like that, too few samples --> too few DMPs/DMRs. Also, my test samples are actually from the same group (controls), so it's not that strange that the groups don't differ. I will test on 16 samples next week (CTRL><case), I will retu ...
written 8 months ago by rasmus.rydbirk10

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