User: Tim Peters

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Tim Peters80
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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 • 36 results • page 1 of 4 • next >
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Comment: C: DMRcate package :How to find the gene associated with coordinate
... 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       ...
written 3 months ago by Tim Peters80
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Comment: C: DMRcate package :How to find the gene associated with coordinate
... 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   ...
written 3 months ago by Tim Peters80
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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 5 months ago by Tim Peters80
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Answer: A: Bumphunting for longitudinal data
... 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 5 months ago by Tim Peters80
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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 11 months ago by Tim Peters80
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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 11 months ago by Tim Peters80
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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 16 months ago by Tim Peters80
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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 18 months ago by Tim Peters80
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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 18 months ago by Tim Peters80
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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 18 months ago by Tim Peters80

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Scholar 15 months ago, created an answer that has been accepted. For A: Bumphunting for longitudinal data
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