User: erfan741

gravatar for erfan741
erfan74130
Reputation:
30
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New User
Location:
London, ON, Canada
Last seen:
7 months ago
Joined:
2 years, 2 months ago
Email:
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Posts by erfan741

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Allele counting tool for a list of known indels from paired end sequencing data
... Most often not. rarely ...
written 7 months ago by erfan74130
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Comment: C: Allele counting tool for a list of known indels from paired end sequencing data
... Yes that s the source of discripancy. For a variant which has a known AF of 0.5, pindel reports the AC an AN of 200 and 1000 sort of thing! ...
written 7 months ago by erfan74130
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Comment: C: Allele counting tool for a list of known indels from paired end sequencing data
... Those other callers do not detect the indels that I want. Pindel was the only one that superseded all in detecting all of my known variants, but it doesnt report the correct AF. I need a tool that give me the correct AF of a known variant. What variant calibration method do you recommend? Even if I ...
written 7 months ago by erfan74130
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Comment: C: Allele counting tool for a list of known indels from paired end sequencing data
... my output is VCF but i want to extract the new metrics from the bam file. The estimates in the VCF file is not accurate. BCFtools reports stats based on what is available in the VCF file. ...
written 7 months ago by erfan74130
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Comment: C: Allele counting tool for a list of known indels from paired end sequencing data
... does it wrk for indels? it says snps only! ...
written 7 months ago by erfan74130
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Allele counting tool for a list of known indels from paired end sequencing data
... I have called a set of indels from paired end sequencing data using pindel, but the reported allele fractions are not accurate. I was womndering if there is a tool available for calculating reference and alternative allele counts for known variants (indels and dups with known break points and known ...
indel pindel sequencing allele counting genotyping written 7 months ago by erfan74130 • updated 7 months ago by btsui290
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Comment: C: Write excel file formatted as Table in R
... No this is not the answer. I want my output as an excel file marked-up as Table inside EXCEL. ...
written 24 months ago by erfan74130
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Comment: C: Write excel file formatted as Table in R
... Yes This is what I want, But I can't find a way of doing that. It s strange that these packages don't have this simple functionality. ...
written 24 months ago by erfan74130
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Write excel file formatted as Table in R
... In Excel, by selecting all the sheet and clicking on "Format as Table" one can change the format of the sheet to table which allows interactive filtering of the columns. How do I generate an excel file using R, with the same formatting? I am using XLSX package in R, but apparently it doesnt have thi ...
table R excel written 24 months ago by erfan74130 • updated 24 months ago by Antonio R. Franco4.0k
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Answer: A: Multivariable linear regression using Limma package; Model Matrix design
... I think I figured it out myself. Apparently this is the only way: pvals<-sapply(1: dim(probe_matrix[1], function(x) eBayes(lmFit(Disease_phenotype, design=model.matrix(~t(probe_matrix[x,])+t(confounding factor))))$p.value) ...
written 2.2 years ago by erfan74130

Latest awards to erfan741

Popular Question 24 months ago, created a question with more than 1,000 views. For Multivariable linear regression using Limma package; Model Matrix design
Student 24 months ago, asked a question with at least 3 up-votes. For Multivariable linear regression using Limma package; Model Matrix design
Scholar 2.2 years ago, created an answer that has been accepted. For A: Multivariable linear regression using Limma package; Model Matrix design

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