User: Tim Triche

gravatar for Tim Triche
Tim Triche4.2k
Reputation:
4,160
Status:
Trusted
Location:
United States
Website:
http://trichelab.vai.org/
Twitter:
@timtriche
Scholar ID:
Google Scholar Page
Last seen:
3 months ago
Joined:
9 years 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 • 424 results • page 1 of 43 • next >
0
votes
1
answer
68
views
1
answer
Fast callback functions for scanTabix?
... 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 ...
tabix written 3 months ago by Tim Triche4.2k • updated 3 months ago by Martin Morgan ♦♦ 22k
0
votes
1
answers
2.7k
views
1
answers
Comment: C: Illumina MethylationEPIC vs. 450K
... 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 22 months ago by Tim Triche4.2k
0
votes
1
answers
1.6k
views
1
answers
Comment: C: Removing sex-chromosome probes from methyLumiSet
... 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 3.1 years ago by Tim Triche4.2k • updated 3.1 years ago by Dan Tenenbaum ♦♦ 8.2k
0
votes
1
answers
1.6k
views
1
answers
Comment: C: Removing sex-chromosome probes from methyLumiSet
... 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 3.1 years ago by Tim Triche4.2k
0
votes
1
answers
1.6k
views
1
answers
Comment: C: Removing sex-chromosome probes from methyLumiSet
... 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 3.1 years ago by Tim Triche4.2k
0
votes
1
answers
1.3k
views
1
answers
Comment: C: Annotation DB for ArrayStar lncRNA arrays
... 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 3.3 years ago by Tim Triche4.2k
0
votes
1
answers
900
views
1
answers
Comment: C: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
... 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 3.5 years ago by Tim Triche4.2k
0
votes
1
answers
426
views
1
answers
Comment: C: How many arrays are "enough" for creating useful fRMA vectors?
... 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 3.6 years ago by Tim Triche4.2k
0
votes
1
answer
426
views
1
answer
How many arrays are "enough" for creating useful fRMA vectors?
... Hi all,   I'm remapping a bunch of hgu133plus2 probes to novel transcripts.  It seems like I need to redefine a number of probesets to do this properly, which is not a big deal, but I also want to use fRMA on the resulting data structure.  I have about 1000 CEL files from roughly comparable tissue ...
annotation frma frmatools written 3.6 years ago by Tim Triche4.2k • updated 3.6 years ago by Matthew McCall820
0
votes
3
answers
522
views
3
answers
Answer: A: "My tags" -- how to actually watch/follow a tag
... thanks all.  one last question, why is the "my tags" field separate from the "watched tags" field?  Historical reasons I suppose.  Anyways, thanks again. ...
written 3.6 years ago by Tim Triche4.2k

Latest awards to Tim Triche

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Interspecies differential expression of orthologs with Edger
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: conceptual question about FDR, FDR adjusted p-value and q-value
Popular Question 2.5 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Popular Question 2.5 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.9 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 296 users visited in the last hour