User: markus.riester

gravatar for markus.riester
Reputation:
110
Status:
Trusted
Location:
Scholar ID:
Google Scholar Page
Last seen:
4 months, 3 weeks ago
Joined:
3 years, 1 month ago
Email:
m*************@novartis.com

Posts by markus.riester

<prev • 86 results • page 1 of 9 • next >
0
votes
1
answer
155
views
1
answers
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 4 months ago by markus.riester110
0
votes
0
answers
186
views
0
answers
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 5 months ago by markus.riester110
0
votes
0
answers
186
views
0
answers
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 6 months ago by markus.riester110
0
votes
0
answers
186
views
0
answers
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 6 months ago by markus.riester110
0
votes
1
answer
108
views
1
answers
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 6 months ago by markus.riester110
0
votes
1
answer
169
views
1
answers
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 6 months ago by markus.riester110
0
votes
1
answer
169
views
1
answers
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 6 months ago by markus.riester110
0
votes
1
answer
155
views
1
answers
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 6 months ago by markus.riester110
0
votes
2
answers
140
views
2
answers
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 6 months ago by markus.riester110
0
votes
1
answer
137
views
1
answers
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 6 months ago by markus.riester110

Latest awards to markus.riester

Scholar 22 months ago, created an answer that has been accepted. For A: Understanding PureCN and its germline SNPs
Scholar 22 months ago, created an answer that has been accepted. For A: Something wrong with my Bioconductor installation? ggtree cannot read any tree
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Understanding PureCN and its germline SNPs

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 219 users visited in the last hour