User: Tim Peters

gravatar for Tim Peters
Tim Peters80
Reputation:
80
Status:
Trusted
Location:
Australia
Last seen:
3 weeks ago
Joined:
4 years, 1 month 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

<prev • 37 results • page 1 of 4 • next >
0
votes
1
answer
1.5k
views
1
answers
Comment: C: DMRcate: incorporating covariates to find DMRs in methylation data?
... Hi Steven, This is indeed possible using datatype="sequencing" - please look at the second half of the vignette for a worked example. Best, Tim *Edit* My bad, I hadn't realised that the example included only contained output from DSS::DMLtest, not DSS::DMLtest.multiFactor. If you use output fro ...
written 4 months ago by Tim Peters80
0
votes
0
answers
250
views
0
answers
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 10 months ago by Tim Peters80
0
votes
0
answers
250
views
0
answers
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 10 months ago by Tim Peters80
0
votes
2
answers
317
views
2
answers
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 12 months ago by Tim Peters80
1
vote
2
answers
317
views
2
answers
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 12 months ago by Tim Peters80
1
vote
3
answers
799
views
3
answers
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 18 months ago by Tim Peters80
0
votes
3
answers
799
views
3
answers
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 18 months ago by Tim Peters80
1
vote
1
answer
503
views
1
answers
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 24 months ago by Tim Peters80
0
votes
3
answers
978
views
3
answers
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 2.1 years ago by Tim Peters80
0
votes
3
answers
978
views
3
answers
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 2.1 years ago by Tim Peters80

Latest awards to Tim Peters

Scholar 23 months ago, created an answer that has been accepted. For A: Bumphunting for longitudinal data
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 247 users visited in the last hour