User: Tim Peters
Tim Peters • 80
- Reputation:
- 80
- Status:
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- Location:
- Australia
- Last seen:
- 2 months, 1 week ago
- Joined:
- 3 years, 11 months 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 Steven,
This is indeed possible using datatype="sequencing" - please look at the second half of the vignette for a worked example.
Best,
Tim
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written 11 weeks ago by
Tim Peters • 80
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... This is a problem with your version of zlib, not DMRcate. Looks like you need to update the version of zlib on your machine. This thread may be of help: https://www.biostars.org/p/89217/
Cheers,
Tim
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written 8 months ago by
Tim Peters • 80
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... The extractRanges() function now appends promoter associations from Gencode/Ensembl instead. I find this annotation more reliable than Illumina's. Have a look at page 4 of the vignette:
https://bioconductor.org/packages/release/bioc/vignettes/DMRcate/inst/doc/DMRcate.pdf
Cheers,
Tim
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written 8 months ago by
Tim Peters • 80
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Comment:
C: Bumphunting for longitudinal data
... Hi Ash,
Yes, it looks like that will work. The ellipsis argument (...) at the end of cpg.annotate() is matched to extra arguments for limma::lmFit(), so block and correlation will propagate to the linear fitting.
And yes, DMRcate can definitely be used for continuous responses as well. The only ca ...
written 10 months ago by
Tim Peters • 80
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... Hi Ash,
Yes, like James said, you'll need to sacrifice some of your covariates to get your design matrix full rank. Once you have a full rank matrix, you can then pass it to cpg.annotate() along with your coefficient of interest (and optionally contrast matrix), and then the regular workflow will d ...
written 10 months ago by
Tim Peters • 80
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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 16 months ago by
Tim Peters • 80
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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 16 months ago by
Tim Peters • 80
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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 22 months ago by
Tim Peters • 80
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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 23 months ago by
Tim Peters • 80
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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 23 months ago by
Tim Peters • 80
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