User: Tim Peters
Tim Peters • 70
- Reputation:
- 70
- Status:
- Trusted
- Location:
- Australia
- Last seen:
- 5 months ago
- Joined:
- 3 years ago
- Email:
- t*******@garvan.org.au
--
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
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... 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
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written 5 months ago by
Tim Peters • 70
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... 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
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written 5 months ago by
Tim Peters • 70
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... 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 10 months ago by
Tim Peters • 70
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... 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 12 months ago by
Tim Peters • 70
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... 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 12 months ago by
Tim Peters • 70
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... 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 12 months ago by
Tim Peters • 70
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... 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
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written 13 months ago by
Tim Peters • 70
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... 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 13 months ago by
Tim Peters • 70
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... 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 14 months ago by
Tim Peters • 70
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... 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 15 months ago by
Tim Peters • 70
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