User: Jimbou

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Jimbou600
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600
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Germany
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2 months ago
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4 years, 1 month ago
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Posts by Jimbou

<prev • 69 results • page 1 of 7 • next >
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Difference of CN probes and SNP probes on genotyping microchip arrays
... Is there a difference between copy number (CN) probes compared to SNP probes on SNP arrays such as the Affymetrix 6.0 SNP array? Physically there could be longer oligos for the CN probes? Do you have to analyse both probes differently, e.g. do tools such as PennCNV use both probes for CNV detectio ...
array affymetrix snp cnv written 7 months ago by Jimbou600 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Loading IMPUTE2 output into R for eQTL analysis
... How you want to treat with the genotype certainity? ...
written 21 months ago by Jimbou600
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Comment: C: I cannot read data into R (read.affy)
... Your data doesn't fit into the `read.table` function. Perhaps it's your header making the problem. Change " " to "_" and try it again. You can also post a snippet of your data table and check the help page for the `?read.affy` function. ...
written 22 months ago by Jimbou600
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Comment: C: PLINK and 1000 Genome browser
... What have you tried so far? Did you checked this [comprehensivs list][1] of tools already? [1]: http://www.1000genomes.org/category/tools/ ...
written 22 months ago by Jimbou600
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Comment: C: CNV analysis for targeted genomic region
... I recommend [R][1] for this. Additional helpful packages are [cn.mops][2], [Gviz][3] or [Exomecopy][4] and some more. You can find a comprehensive list in this nice paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S11-S1 [1]: https://cran.r-project.org/ [2]: htt ...
written 23 months ago by Jimbou600
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Comment: C: CNV analysis for targeted genomic region
... You could try to calculate the coverage per gene/exon/target, median normalize over all/within sets, build a reference sample supposed to be copy number of two, calculate the ratio between target and reference sample and perform a cluster analysis for CNV detection per gene/exon/target. This is simi ...
written 23 months ago by Jimbou600
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Answer: A: Imputation for genotyping data
... As inferred in this [paper][1] > In principle, a phasing algorithm should be able to “learn” about desirable phasing configurations for a given study individual by pooling information across the reference panel and all other individuals in the study, and the phasing accuracy should increase wit ...
written 23 months ago by Jimbou600
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Comment: C: What is the best method for determining copy number of a specific gene (from sal
... For this targeted, not genome-wide approach you can use TaqMan copy number assays. There are many pre designed assasy for mouse and humans available. RNaseP is the reference gene most people use. ...
written 2.1 years ago by Jimbou600
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Comment: C: Good way of plotting a statistic with error bars
... Perhaps a forest plot? But also similar to @Alex answer using points, lines or segments. ...
written 2.1 years ago by Jimbou600
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Comment: C: CYP2D6 alleles determination
... Of course this can happen. If that pattern occurs in a population frequently (>1-5%), smart people will give this combination a new name. Otherwise this is a rare genotype. Haplotype analysis would be the next keyword. ...
written 2.2 years ago by Jimbou600

Latest awards to Jimbou

Teacher 5 months ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Great Question 6 months ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Supporter 7 months ago, voted at least 25 times.
Great Question 17 months ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Popular Question 17 months ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Student 17 months ago, asked a question with at least 3 up-votes. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 21 months ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Popular Question 2.2 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Scholar 2.2 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Scholar 2.2 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Scholar 2.2 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 2.3 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Partial or complete overlap of two genomic ranges
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 2.9 years ago, created an answer that has been accepted. For A: GVIZ plotTracks plots dense features under each other
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Student 3.5 years ago, asked a question with at least 3 up-votes. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Commentator 3.9 years ago, created a comment with at least 3 up-votes. For C: Jointly Detect Somatic Copy Number Variations

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