Moderator: Obi Griffith

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Obi Griffith15k
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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

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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 3 months ago by Obi Griffith15k
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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 3 months ago by Obi Griffith15k
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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 3 months ago by Obi Griffith15k
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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 3 months ago by Obi Griffith15k
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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 3 months ago by Obi Griffith15k
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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 5 months ago by Obi Griffith15k
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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 5 months ago by Obi Griffith15k
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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 5 months ago by Obi Griffith15k • updated 5 months ago by WouterDeCoster20k
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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 6 months ago by Obi Griffith15k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... Yes. Just look at the format of the "mutation_data" object. If you can add another column with VAF values then you should be able to just specify mainLabelCol="X" where X is the name of your new VAF column rather instead of "amino.acid.change". ...
written 7 months ago by Obi Griffith15k

Latest awards to Obi Griffith

Gold Standard 12 days ago, created a post with more than 25 bookmarks. For Analysing Microarray Data In Bioconductor
Great Question 5 weeks ago, created a question with more than 5,000 views. For Isaac Asimov Accurately Predicts Woes Of Bioinformatician
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
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Popular Question 4 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Student 5 months ago, asked a question with at least 3 up-votes. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
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Popular Question 9 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Popular Question 11 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Great Question 11 months ago, created a question with more than 5,000 views. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Great Question 12 months ago, created a question with more than 5,000 views. For How Much Coverage Do We Need For An Rna-Seq Experiment?
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Popular Question 13 months ago, created a question with more than 1,000 views. For Consent and privacy issues arising from the sequencing of cell lines

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