Moderator: Obi Griffith

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Obi Griffith17k
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Location:
Washington University, St Louis, USA
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http://www.obigriffith...
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obigriffith
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Last seen:
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I am an Assistant Professor of Medicine (Oncology) and Genetics at Washington University School of Medicine and Assistant Director at the McDonnell Genome Institute. I study cancer genomics, primarily through clinical statistics and bioinformatic analyses of next-generation sequence data such as whole genome (WGS), exome, and transcriptome (RNA-seq) data.

Posts by Obi Griffith

<prev • 419 results • page 1 of 42 • next >
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Answer: A: Paternity Testing from WGS Trio
... It is definitely *possible* to assess paternity from whole genome sequence (WGS) data. Paternity can probably be established with as little as a few dozen or maybe hundreds of well-chosen single nucleotide polymorphisms (SNPs). If you have decent WGS data you can expect to genotype millions of SNPs. ...
written 6 months ago by Obi Griffith17k
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... postimages.org has been having some issues with their hosting service (and business model for that matter). The domain name postimg.org was apparently locked by registry. They moved to postimg.cc. Once I updated the urls they returned. BioStars developers have been informed about this as I suspect i ...
written 10 months ago by Obi Griffith17k
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Still there for me. This sounds like a BioStars or system-specific issue? ...
written 11 months ago by Obi Griffith17k
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Comment: C: Database Of Tumor Suppressors And/Or Oncogenes
... I feel like, right now, the best answer to this question is the Cancer Gene Census. They currently provide a TSV download of their complete list of 567 genes with nearly all being indicated as oncogene and/or tumor suppressor (TSG). ...
written 19 months ago by Obi Griffith17k
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Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... Please note that the trainset_gcrma.txt and testset_gcrma.txt can change over time if using different versions of the custom CDF annotations. The clindetails.txt files should be static. I don't know why that command doesn't work. It seems like there are regularly issues with GEO services failing or ...
written 23 months ago by Obi Griffith17k
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Comment: C: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random F
... This happens because over time the custom CDF files change so that hardcoded number to eliminate AFFX (control) probes becomes incorrect. It is then possible that some of these get included in the model. We added the alternative way to remove AFFX probes in some places but missed others and this lik ...
written 23 months ago by Obi Griffith17k
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Comment: C: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random F
... @debitboro - welcome to Biostars. The predict function will only use predictor variables that exist in the (previously trained) model that is provided. Running most recently, I get 1247 predictors after filtering the training data down from 12264 total predictors. The RF model is trained on, and onl ...
written 23 months ago by Obi Griffith17k
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Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... All of the files can be found here: https://github.com/obigriffith/biostar-tutorials/tree/master/MachineLearning. The file you are specifically looking for could be downloaded here: https://raw.githubusercontent.com/obigriffith/biostar-tutorials/master/MachineLearning/trainset_clindetails.txt ...
written 23 months ago by Obi Griffith17k
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Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... The general principles are the same but this tutorial (part 1) is really focused on preparing a datafile from microarray data. You will want to use an alternative approach to create a file that is analogous to datafile="trainset_gcrma.txt". This would be a simple matrix of gene (or transcript or oth ...
written 23 months ago by Obi Griffith17k
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Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... You are indeed correct that GC/AT content correlates with Alu elements. In general Alu elements seem to be correlated with more GC-rich regions, although it depends on the type/age of the Alu element (and is probably [more complicated][1] than that). Indeed the very top track in the IGV snapshot sho ...
written 2.1 years ago by Obi Griffith17k

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