Moderator: Obi Griffith

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Obi Griffith15k
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Washington University, St Louis, USA
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http://www.obigriffith...
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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 • 416 results • page 1 of 42 • next >
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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 days 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 5 days 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 5 days 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 5 days 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 5 days 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 11 weeks 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 11 weeks 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 11 weeks ago by Obi Griffith15k • updated 11 weeks ago by WouterDeCoster16k
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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 3 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 4 months ago by Obi Griffith15k

Latest awards to Obi Griffith

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Student 11 weeks ago, asked a question with at least 3 up-votes. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 6 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Popular Question 8 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Great Question 8 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 9 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Great Question 9 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 9 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Scholar 9 months ago, created an answer that has been accepted. For A: What read lengths are produced by modern Illumina sequencers?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 10 months ago, created a question with more than 1,000 views. For Consent and privacy issues arising from the sequencing of cell lines
Popular Question 10 months ago, created a question with more than 1,000 views. For Consent and privacy issues arising from the sequencing of cell lines
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?

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