User: Shixiang

gravatar for Shixiang
Shixiang30
Reputation:
30
Status:
New User
Location:
Shanghai
Website:
http://www.shixiangwan...
Twitter:
ShixiangWang
Last seen:
2 weeks, 2 days ago
Joined:
9 months, 2 weeks ago
Email:
s***************@gmail.com

Posts by Shixiang

<prev • 22 results • page 1 of 3 • next >
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Comment: C: how to normalize chromosome arms?
... I also have this question ...
written 16 days ago by Shixiang30
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Comment: C: Are TCGA data from UCSC cancer browser and TCGAbiolinks different?
... the legacy TCGA data came from hg19 version and TCGA data from the GDC now use hg38 version. therefore, it will have some difference. ...
written 4 weeks ago by Shixiang30
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Answer: A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
... I am also looking for this, and I find all what we need are included in package GWASTools https://www.rdocumentation.org/packages/GWASTools/versions/1.18.0/topics/centromeres ...
written 4 weeks ago by Shixiang30
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Comment: C: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
... However, hg38 version cannot find centromeres in this way ...
written 4 weeks ago by Shixiang30
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Comment: C: TCGA CNV Files
... Hello, I want to know how TCGA get the "nocnv" file. I download "masked copy number" data from TCGA, it says "Masked copy number segments are generated with the same method except that a filtering step is performed that removes Y chromosome and probe sets that were previously indicated to have freq ...
written 4 weeks ago by Shixiang30
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Comment: C: Protocol To Downlad TCGA Data From GDC
... Does someone know how to fix this error? 92% [##########################ERROR: Max retries exceeded.:02:27 16.23 MB/s ERROR: Max retries exceeded. ERROR: Max retries exceeded. ERROR: Max retries exceeded. ...
written 5 weeks ago by Shixiang30
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Cannot reproduce ABSOLUTE example result
... I want to use ABSOLUTE, so I read documentation at http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ABSOLUTE and run example data (solid_tumor) by GenePattern ABSOLUTE modules. However I cannot reproduce this result. I set parameters following > The dataset samples ar ...
absolute written 6 weeks ago by Shixiang30
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Answer: A: What is the meaning of copy_ratio in reviewed result of ABSOLUTE
... I captured function `MakeSegObj` calculate copy number as `2 ^ Segment_Mean` but not `2 * 2^ Segment_Mean`. I think this code is not right because the former means `copy number ratio`. The real problem is that at the end, ABSOLUTE calculate `copy_ratio` as `copy_number / 2`, which generated results ...
written 6 weeks ago by Shixiang30
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What is the meaning of copy_ratio in reviewed result of ABSOLUTE
... I downloaded ABSOLUTE example data from . When I checked the input segment file and result data, I find very confusing column marked as "copy_ratio". > segtab2 = readr::read_tsv("~/Downloads/ABSOLUTE exampledata/1131213/solid_tumor.segtab.txt") > head(segtab2) # A tibble: 6 x 1 ...
absolute written 6 weeks ago by Shixiang30
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(Closed) difference between total and allelic copy number
... Could someone explain the difference between total and allelic copy number? I am very confused. ...
cnv written 6 weeks ago by Shixiang30

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