User: Lemire/OICR

gravatar for Lemire/OICR
Lemire/OICR350
Reputation:
350
Status:
Trusted
Location:
Canada
Twitter:
@CELLULOID_R
Last seen:
9 months, 3 weeks ago
Joined:
1 year, 11 months ago
Email:
m*************@oicr.on.ca

Posts by Lemire/OICR

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Is okay to apply ANOVA to Log2 transformed data ?
... If you are concerned about the underlying parametric assumptions, you could try Kruskal-Wallis, the non-parametric version of the ANOVA. It's rank-based, meaning you can apply it to the non-transformed data. ...
written 9 months ago by Lemire/OICR350
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Answer: A: Whole exome sequencing data, rare variants and QQ-plots
... QC has likely nothing to do with your problem. Here are two things you need to think about: (1) you're using a 2df test (genotypic?) for rare variants even though some of your cell counts are likely to be 0. (2) You're using a qq-plot designed to assess the distribution of a continuous variable whe ...
written 14 months ago by Lemire/OICR350
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Answer: A: Bioinformatics analyses hall of shame
... Just go to https://pubpeer.com/ ...
written 15 months ago by Lemire/OICR350
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Answer: A: How to Assess Paired Sample Data from WES
... This is an answer to the question you actually asked: Look up http://genome.sph.umich.edu/wiki/VerifyBamID ...
written 15 months ago by Lemire/OICR350
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Answer: A: Why are there too many mutations in controls, but not in tumour?
... That's probably loss of heterozygosity, not somatic substitutions. Caused by chromosomal regions where one parental copy was loss in the tumor (i.e. deleted). Check if they tend to cluster in regions. ...
written 16 months ago by Lemire/OICR350
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Answer: A: IGV not showing the variants detected by GATK and Varscan
... Try playing with the viewing options under the "Alignment" tab under Preferences (or similar for your OS).  In particular, uncheck the "Downsample reads" box.   ...
written 20 months ago by Lemire/OICR350
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Answer: A: LOD score of a single genotype
... It's been over 10 years I dealt with linkage, but let me have a try... To illustrate, I downloaded the test examples (datafile.dat and pedfile.dat) at http://bioinfo.cs.technion.ac.il/superlink/ I modified the last two line of datafile.dat: 0.0000 << RECOMBINATION VALUES 1 0.0500 0.50000 &l ...
written 20 months ago by Lemire/OICR350
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Answer: A: BWA mem how to know if a read is mapped uniquely?
... I am using version 0.7.12 and bwa mem reports the XA tag (fake data): % bwa mem fake.fa  fake.fq    [M::bwa_idx_load_from_disk] read 0 ALT contigs @SQ     SN:fakechr1     LN:1500 @SQ     SN:fakechr2     LN:1500 @PG     ID:bwa  PN:bwa  VN:0.7.12-r1039 CL:bwa mem fake.fa fake.fq [M::process] read 1 ...
written 20 months ago by Lemire/OICR350
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Answer: A: Armitage's trend test for the 2x3 genotype table
... The Armitage test for trend only has one parameter, hence one degree of freedom.  If you code your genotypes 0,1 and 2, then implicitly the odds ratio for homozygous is assumed to be the square of the heterozygous one. Other codings of genotypes lead to different relationships between the odds ratio ...
written 20 months ago by Lemire/OICR350
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Comment: C: Are there any tools like "Somatic variation Viewer" ? (like IGV)
... Load both tumor and normal bam files in IGV?  ...
written 21 months ago by Lemire/OICR350

Latest awards to Lemire/OICR

Popular Question 14 months ago, created a question with more than 1,000 views. For CELLULOID: tumor ploidy, cellularity, subclonal copy number events
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 22 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 23 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ

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