User: CY

gravatar for CY
CY550
Reputation:
550
Status:
Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
7 hours ago
Joined:
5 years ago
Email:
c********@hotmail.com

Posts by CY

<prev • 271 results • page 1 of 28 • next >
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Wilcoxon test, t-test and negative binomial test for DEG of scRNA-Seq data
... I tried Wilcoxon test, t-test and negative binomial test across different amount of cells (biological replicates) (3, 6, 10, 50, 100, 500) derived from scRNA-Seq data. My intuition is that, since Negative Binomial distribution can better describe the expression distribution, it can detect more DEG t ...
scrna-seq deg differential expression written 6 days ago by CY550
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Comment: C: Treat methylation as binary or continuous signal when detecting DMR?
... I came across your post earlier. Is there a concensus on the preference of whether treat it as binary or continous? In another word, Is there a concensus on the preference of whether defining DMC (binary value on each site) or DMR (continuous value across region)? What are the pros and cons between ...
written 5 weeks ago by CY550
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Treat methylation as binary or continuous signal when detecting DMR?
... Methylation level is usually measured as continuous value (M-value from 450K). However, DNA methylation is binary outcome in nature (methylated or not), and it is relatively easy to make the conversion since methylation is bimodal around 0.2 and 0.8. 1: When we are to detect DMR (region) or DMS (s ...
methylation written 6 weeks ago by CY550
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Comment: C: What statistical test for CpG DMR ?
... Hi Devon, regarding the 2nd point, do you think negative hypergeometric distribution is a proper chioce (similar logic of using NB distribution in DE instead of Poisson distribution)? ...
written 6 weeks ago by CY550
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Is definition of differentially methylated region (DMR) biologically meaningful?
... I am aware that many studies use DMR to measure methylation level / region. However, DNA methylation impose its impact by suppressing gene expression. When we try to measure the magnitude / consequence of DNA methylation, should not we consider more about the correlation between methylation and mRNA ...
methylation dmr written 6 weeks ago by CY550 • updated 6 weeks ago by Hamid Ghaedi500
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Comment: C: Defining methylation level of CpG island
... Methylation level is measured as per CpG site (probe). However, we usually want to know the impact of entire promoter on corresponding gene. So we need to somehow summarized the methylation level of each CpG site into the methylation level of corresponding gene. Is there a widely accepted way to do ...
written 6 weeks ago by CY550
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Defining methylation level of CpG island
... Differentially methylated site is technically measured by each probe. However, CpG island within gene promoter is comprised of numerous probes. Do we have a consensus of how to determine the methylation level of the entire CpG island (or entire promoter) given the methylation of each probe within th ...
cpg island methylation written 6 weeks ago by CY550
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Comment: C: How to derive sequence of novel transcript identified by Cufflinks
... Yes, it is reference guided. ...
written 7 weeks ago by CY550
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How to derive sequence of novel transcript identified by Cufflinks
... I am new to transcript level analysis using RNA-Seq. The goal is to retrieve sequence of newly identified transcript from RNA-Seq data. We just finished runing Cufflinks and seems like that a number of putative novel transcripts were generated. What do I have to do to further retrieve the sequence o ...
transcript rna-seq written 7 weeks ago by CY550
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Did and why recent studies show superior predictive power using methylation data on early cancer detection
... There seems to be an increasing tend (in both academic and industry) of using methylation pattern for cancer detection / classification. It almost feels that methylation is superior on such task over other omics (somatic mutation or RNA expression). What I can think of this is: 1. Methylation data ...
cancer detection methylation written 3 months ago by CY550

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