Moderator: Obi Griffith

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Obi Griffith16k
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Washington University, St Louis, USA
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obigriffith
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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 • 417 results • page 1 of 42 • next >
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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 3 months ago by Obi Griffith16k
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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 7 months ago by Obi Griffith16k
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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 7 months ago by Obi Griffith16k
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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 7 months ago by Obi Griffith16k
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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 7 months ago by Obi Griffith16k
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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 7 months ago by Obi Griffith16k
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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 9 months ago by Obi Griffith16k
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Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... Thanks for the comments! 1. I don't think this has to do with a general Alu repeat low complexity, low mapping quality issue. The reads in these peaks and both reads of the discordant pairs almost entirely have normal (very good) mapping qualities. In any case, if it just had to do with mapping is ...
written 9 months ago by Obi Griffith16k
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Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS data
... OK. I realize this is not exactly a bioinformatics question but I know that a lot of people in this forum spend their days staring at NGS alignments and am hoping someone has an explanation or some insight. See the IGV screenshot below of representative matched tumor and normal samples. The pattern ...
wgs ngs alignment sequencing written 9 months ago by Obi Griffith16k • updated 9 months ago by WouterDeCoster23k
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Comment: C: Plotting numbers of somatic substitutions per megabase (MB)
... Are you supplying the Alexandrov example just to demonstrate layout? I ask because this figure has a lot more going on than just mutations/MB. It is showing mutations/MB brokend down by mutation type in several different ways. If that is what you want then it is a complicated question/answer. ...
written 10 months ago by Obi Griffith16k

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