User: markus.riester

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Posts by markus.riester

<prev • 88 results • page 1 of 9 • next >
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Answer: A: callLOH output file NA values
... Yes, the callLOH function changed and I actually mention this in the NEWS file ( http://bioconductor.org/packages/release/bioc/news/PureCN/NEWS ). LOH calling requires heterozygous SNPs, so NA means no SNPs. The change of defaults was necessary because some users were not aware that segments witho ...
written 3 months ago by markus.riester110
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Answer: A: PureCN.R warning "duplicate keys in header will be forced to unique rownames"
... No, these should be benign. I'll hide these after the next Bioconductor release next week. ...
written 3 months ago by markus.riester110
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Answer: C: Chromosome arm loss and --maxhomozygousloss default
... It means that homozygous losses are not accepted in the optimization when the corresponding segment is larger than 10Mb or when more than 5% of a chromosome (whole chromosome, not arm) is completely lost. This is mainly to avoid wrong solutions where a complete chromosome is assigned to a homozygous ...
written 8 months ago by markus.riester110
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Comment: C: Issue with BiocParallel
... Do you mind trying version 1.13.4? It should balance the workload much better across nodes. This should reduce the runtime significantly and might decrease the chance of such communication errors. ...
written 9 months ago by markus.riester110
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Comment: C: Issue with BiocParallel
... Is it possible that this happens when a worker was idle for a long time? Some workers exit early after a few minutes, other can run for more than our in big datasets. This is something I can probably find an easy workaround for. ...
written 10 months ago by markus.riester110
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Comment: C: Issue with BiocParallel
... Thanks Martin and Milos. There is definitely some room for improvement, although I've never seen this error even in our whole exomes. Martin, is there an easy way to profile the memory usage of workers? ...
written 10 months ago by markus.riester110
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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 10 months 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 10 months 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 10 months 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 months ago by markus.riester110

Latest awards to markus.riester

Popular Question 8 months ago, created a question with more than 1,000 views. For Annotate VCFs with Cosmic (ExAC etc.) fields
Scholar 2.2 years ago, created an answer that has been accepted. For A: Understanding PureCN and its germline SNPs
Scholar 2.2 years ago, created an answer that has been accepted. For A: Something wrong with my Bioconductor installation? ggtree cannot read any tree
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Understanding PureCN and its germline SNPs

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