User: Tim Peters

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Tim Peters60
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Tim Peters, PhD

Bioinformatics Research Officer | Epigenetics Research Laboratory | Genomics and Epigenetics Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

Posts by Tim Peters

<prev • 32 results • page 1 of 4 • next >
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Comment: C: DMRcate results cg ID of significant DMR
... Hi Giovanni, Any post-filtering decision is up to you - I've made DMRcate that way so user can have some control over what thresholding they believe is best. Many users I've encountered have made decisions in line with what you describe in your bullet points. Best, Tim ...
written 4 days ago by Tim Peters60
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Comment: C: DMRcate results cg ID of significant DMR
... Hi Poojitha, Looks like the S4 structure of IlluminaHumanMethylationEPICanno.ilm10b2.hg19 has changed. Try locs <- IlluminaHumanMethylationEPICanno.ilm10b2.hg19::Locations for the first line instead.  Cheers, Tim ...
written 4 days ago by Tim Peters60
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Answer: A: DMRcate results file ordered by genomic location and not Stouffer p-val?
... Hi elleno, Thanks for picking this up - we rewrote dmrcate() recently to speed it up a bit, but looks like we neglected to reorder the DMRs. I have put the fix in svn and it should propagate to the web within 48 hours, or you can grab the corrected version right now at https://github.com/timpeters8 ...
written 5 months ago by Tim Peters60
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Answer: A: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Hi Rahel, Well, it says "Partial NA coefficients for 1 probe(s) " now instead of the 61,723 you had before, so that's progress. This means there is only one row in the matrix for which the model is inestimable.  I would check a few more things about mVals, you'll need to remove rows that have any ...
written 7 months ago by Tim Peters60
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Come to think of it, it is vital that you name your column(s) in contMatrix, and then pass a column name to coef in your call to cpg.annotate(). Otherwise it will simply take the first column of design as your coefficient of interest, which I assume is not what you want. Look at what Jenny has done: ...
written 7 months ago by Tim Peters60
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Answer: A: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Dear Rahel, At this point it's likely you have NAs in your mVals matrix giving you your partial NA coefficients. Please check the values in your matrix to make sure there aren't any. If this isn't the case, the only other problem I can forsee is that the mVals are enormous in both directions, which ...
written 7 months ago by Tim Peters60
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Answer: A: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Hi Jenny,  Thanks for spotting this. Looks like I didn't put all my match.arg()s in! I have updated the git and svn, and the fix should propagate to the master within 48 hours. Thanks again, Tim ...
written 7 months ago by Tim Peters60
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Answer: A: minfi, lumi, methylumi, DMRcate installation error
... Hi Poojitha, To further James' comment, I would remove these two lines from your workflow > library(IlluminaHumanMethylation450kanno.ilmn12.hg19) > library(minfi) since DMRcate already attaches minfi when you load it, and then cpg.annotate (via minfi) will attach the annotation package whe ...
written 8 months ago by Tim Peters60
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Answer: A: DMRcate: Scaling factor for bandwidth
... Hi Alex, I haven't done any empirical testing on the distribution of EPIC CpGs but I'd wager the optimum is about the same. The real issue is when you're doing sequencing assays, and fitting genomically consecutive CpGs, that you have to make C a lot larger, which makes the kernel smaller.  If you ...
written 9 months ago by Tim Peters60
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Answer: A: DMRcate DMR.plot Turn Off Group Means
... Hi Chris, Thanks, I would definitely encourage you and other users to fork DMR.plot() for your own purposes. There are a myriad of ways to visualise methylation, and DMR.plot() is provided as a) a sanity check and b) a starting point for users to fool around with Gviz, rather than being a wrapper f ...
written 10 months ago by Tim Peters60

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