## User: Tim Triche

Tim Triche4.2k
Reputation:
4,160
Status:
Trusted
Location:
United States
Website:
http://trichelab.vai.org/
@timtriche
Scholar ID:
Last seen:
1 month, 1 week ago
Joined:
9 years, 2 months ago
Email:
t*********@gmail.com

Assistant Professor of Bioinformatics, Van Andel Research Institute

Adjunct Professor of Translational Genomics, University of Southern California

Founding Partner, Anamnesis LLC

#### Posts by Tim Triche

<prev • 426 results • page 1 of 43 • next >
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... sessionInfo() output breaks the 5000 character limit (of course...)  `R R> sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)     Matrix products: default BLAS: /primary/vari/software/R/R-3.5.0/lib64/R/lib/libRblas.so LAPACK: ...
written 5 weeks ago by Tim Triche4.2k
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... What does this mean? And why is it nearly impossible to get this to work? I have cleared the cache, taken various suggestions from ExperimentHub/BiocManager, and none of it helps. This... kind of sucks, to be honest. install("sesameData", localHub=TRUE) Bioconductor version 3.8 (BiocManager 1.30 ...
written 5 weeks ago by Tim Triche4.2k • updated 5 weeks ago by Martin Morgan ♦♦ 22k
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... This is one of those things I imagine *somebody* must have done, but I'm not finding an example of it.  In order to side-step compatibility issues between mac/windows/linux and also allow for reading of enormous (hundreds of millions to billions of loci from hundreds of subjects) files from (wait fo ...
written 5 months ago by Tim Triche4.2k • updated 5 months ago by Martin Morgan ♦♦ 22k
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... You might also consult http://biorxiv.org/content/early/2016/07/23/065490 Since the results I have seen from Partek users sometimes suggests they are constrained by the software when analyzing methylation data. On the other hand, if you have a straightforward single platform experiment, that may ...
written 2.0 years ago by Tim Triche4.2k
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... Hmmm, that's a featureFilter issue, but something I could fix... let me see if I can patch that and the methylumIDAT docs at the same time. Looks like I'll be writing a lot of patches today (i.e. the ones I wanted to write for ozymandias and DMRcate, and these) ...
written 3.2 years ago by Tim Triche4.2k • updated 3.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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... 1) why would you want to toss out the X chromosome?  There are an awful lot of sites on chrX that matter 2) why not add a term for gender in the regression fit / DMRcate / whatever instead? 3) why not check that the sex of samples (from X copy number and/or X inactivation) matches the putative sex ...
written 3.3 years ago by Tim Triche4.2k
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... 1) that's a GoldenGate example, there are no chrY probes on that platform 2) here is a vignette-length 450k example for methylumIDAT (which I should point to, now that you mention it, in the man page for methylumIDAT): http://www.bioconductor.org/packages/release/bioc/vignettes/methylumi/inst/doc/m ...
written 3.3 years ago by Tim Triche4.2k
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... Actually it would be nice to use ENSEMBL/lncipedia mappings. From my experience they are the most useful. Maybe dr Coombes has observations to the contrary but I've looked at the OSU lncRNA array data and mapping those IDs was not easy! I think I know exactly which dataset is pissing you off, in fac ...
written 3.5 years ago by Tim Triche4.2k
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... Did you use the barcodes or the SCAN/fRMA corrected estimates for your classifications?  Just curious. It seems like SCAN.UPC is ultimately a bit more flexible than the current incarnation of fRMA for completely reannotated arrays (unpublished observations of my own, which with any luck will eventu ...
written 3.6 years ago by Tim Triche4.2k
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... Well, I don't have any technical replicates between batches, but it looks like 5-10 batches of 100-200 arrays should work well enough. I'm just porting a technique from the Liu lab that I want to mechanize on a few thousand arrays with reproducible results. fRMA/barcoding seems like the easiest way ...
written 3.8 years ago by Tim Triche4.2k

#### Latest awards to Tim Triche

Popular Question 5 months ago, created a question with more than 1,000 views. For Interspecies differential expression of orthologs with Edger
Popular Question 5 months ago, created a question with more than 1,000 views. For MethyLumiSet object
Popular Question 5 months ago, created a question with more than 1,000 views. For Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Interspecies differential expression of orthologs with Edger
Popular Question 2.7 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Popular Question 2.7 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: conceptual question about FDR, FDR adjusted p-value and q-value
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.1 years ago, created 100 posts.

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