User: markus.riester

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Posts by markus.riester

<prev • 82 results • page 1 of 9 • next >
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Answer: A: Copy ratio close to but not exactly 1
... There is a log-ratio calibration step that shifts the log-ratios slightly up or down in the likelihood model. This happens when the measured log-ratios do not properly align to integer copy numbers. There can be various reasons for this, but it most often happens in small panels when major copy numb ...
written 1 day ago by markus.riester110
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Comment: C: Assigning DUP/DEL p-value to CNV segment
... This works probably well for larger segments, but you assume a constant variance and ignore the fold-change. Using something like voom will incorporate the variance observed in the pool of normals and the variance due to coverage. It might be ok, the log-ratios are cleaned of most noise we can get r ...
written 8 days ago by markus.riester110
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Answer: A: Assigning DUP/DEL p-value to CNV segment
... Yes, you want the coverage, not the variant log-ratios. Usually less than 15% of exons (num.marks in DNAcopy output) have variants, so you would ignore most information.  You can probably use something like voom to compare the tumor coverage against all normals in the database. This will incorporat ...
written 9 days ago by markus.riester110
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Answer: A: Copy ratio threshold for calling actual CNV
... We use the callAlterations output, with homozygous deletions called as deletion and amplifications called as copy number >= 6 when focal and ploidy < 4 and >=7 otherwise. But these cutoffs are always hand wavy. For some genes, smaller copy number gains can be quite significant (I cannot fin ...
written 10 days ago by markus.riester110
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Answer: A: Mutation Burden file and manual curation
... It affects the posterior probabilities of the germline vs somatic classification, but these are fairly robust to errors in purity and ploidy. So if you don't see a difference, that's not unexpected.  ...
written 15 days ago by markus.riester110
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Answer: C: PureCN Solution Heatmap values
... Yes, the matrix is an approximation that does not try to assign integer copy numbers to segments yet. The idea is to start the Markov chain at various places that are likely close to local optima - the fitness landscape of this problem is so spiky it's hard to get a good mixing chain otherwise. The ...
written 16 days ago by markus.riester110
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Answer: A: CNV in Normal Samples?
... I would use specialized tools for germline. We use a very similar coverage normalization as GATK4 and this comes with a germline workflow. But there are many others.  If you really want to use PureCN, make sure that the normal is not in the pool and do not provide a target weights file (for somatic ...
written 25 days ago by markus.riester110
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Answer: A: PureCN recover optimum solution
... I think you can simply delete the CSV file and re-run PureCN.R with --rds sample.rds. It should re-create the original CSV file.  ...
written 8 weeks ago by markus.riester110
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Answer: A: PureCN PureCN.R --rds option recreate all output files?
... Yes, if you run it with --rds, it will open the CSV file, pick the solution closest to the there specified purity/ploidy combination and re-create all PureCN.R output files (instead of the default of creating the output for the maximum likelihood solution). ...
written 8 weeks ago by markus.riester110
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Comment: C: PureCN Manual Curation .rds file
... It won't change the RDS, but this shouldn't be necessary. If you need the RDS in R (outside the command line tools), simply load it with readCurationFile instead of readRDS and you should be fine. ...
written 8 weeks ago by markus.riester110

Latest awards to markus.riester

Scholar 15 months ago, created an answer that has been accepted. For A: Understanding PureCN and its germline SNPs
Scholar 15 months ago, created an answer that has been accepted. For A: Something wrong with my Bioconductor installation? ggtree cannot read any tree
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Understanding PureCN and its germline SNPs

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