User: asyavuz

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asyavuz130
Reputation:
130
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Trusted
Location:
UK
Last seen:
1 year, 9 months ago
Joined:
4 years, 9 months ago
Email:
a**********@sabanciuniv.edu

Posts by asyavuz

<prev • 4 results • page 1 of 1 • next >
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Comment: C: visualization of DMRcate or minfi output on UCSC
... This may sound too obvious, but did you try uploading directly to the UCSC genome browser? Is your file too big? ...
written 22 months ago by asyavuz130
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Answer: A: visualization of DMRcate or minfi output on UCSC
... Hi Rahel, You can export a GRanges object from DMRcate output with "extractRanges" function. After you get your Granges object, you can use rtracklayer library's "export.bed" function. Then you can add that BED file as a custom track on UCSC (under My Data menu). For minfi DMPs, you first need to ...
written 22 months ago by asyavuz130
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Answer: A: B-Values and M-Values
... You may start by reading [this article][1]. It will give you the necessary background in understanding why and when M-value should be preferred. You can easily calculate M-values from B-values or vice versa. And again, this paper has the necessary formulas in it. Good luck! [1]: https://bmcbioi ...
written 22 months ago by asyavuz130
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Answer: A: ChAMP error in EPIC data import
... Actually, I traced this error back to wateRmelon, due to relatively recent minfi update. Downgrading Biobase wouldn't work as minfi changed their base objects for RGChannelSet, MethylSet, and RatioSet from eSet to SummarizedExperiment starting from v1.21, some of the inherited functions are changed. ...
written 22 months ago by asyavuz130

Latest awards to asyavuz

Scholar 22 months ago, created an answer that has been accepted. For A: ChAMP error in EPIC data import
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: visualization of DMRcate or minfi output on UCSC
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: ChAMP error in EPIC data import
Appreciated 22 months ago, created a post with more than 5 votes. For A: ChAMP error in EPIC data import
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: ChAMP error in EPIC data import

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