User: CY

gravatar for CY
CY270
Reputation:
270
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Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
2 weeks, 5 days ago
Joined:
3 years, 4 months ago
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Posts by CY

<prev • 175 results • page 1 of 18 • next >
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Why can't solve tumor clonality using simple EM (Gaussian mixture) instead of MCMC(PyClone) or variational Bayes (SciClone)?
... SciClone uses variational Bayes; an extension of EM. PyClone uses MCMC; an alternative to variational Bayes. Both method are related to, but more complicated than EM. Why can't we just use EM (Gaussian mixture) to do this (latent variables is the 'membership' of each variant with specified VAF to ...
clonality sciclone pyclone written 5 weeks ago by CY270
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Can we get absolute abundance of TCR using TCR-Seq?
... I have a project in which I want to compare the **absolute abundance** of TCR across patients. I have no problem deriving relative abundance of each TCR using TCR-Seq. How about absulote abundance? With DNA barcode, we can calculate the amount of original fragment before PCR. Beside, I can use th ...
tcr-seq written 6 weeks ago by CY270
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Comment: C: Is linearity maintained in linear regression of RNA-Seq?
... Even though logCPM (voom) transformed expression value maintains linearity, we still face 0-sum game issue which cause variables dependence and non-linearity, right. This issue is inherited in the raw data and I can't see any way to fix it. ...
written 7 weeks ago by CY270
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Comment: C: Is linearity maintained in linear regression of RNA-Seq?
... Thanks Kevin. If I understand you correctly, the methods you suggest normalizes library size and make the counts more normally distributed. However, The 0-sum game nature of RNA-Seq library still causes varibles dependency and non-linear relationship. Would it compromise linear model a lot? ...
written 8 weeks ago by CY270
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Is linearity maintained in linear regression of RNA-Seq?
... Linear regression is used in cell type decomposition (TIMER or CIBERSORT). I am wondering if the linearity assumption met during modeling. 1. I imagine raw count is not eligible because different library size causes non-linearity. Log-transformed value probably cause non-linearity as well, right? ...
rna-seq written 8 weeks ago by CY270 • updated 8 weeks ago by Kevin Blighe37k
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Comment: C: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... Hi Ryan. I am still a bit confused about how would such 0-sum game causes non-linearity. This may cause some sort of dependency between variables but the overall expression is still the weighted sum of expression of its components (different cell type), right? ...
written 8 weeks ago by CY270
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Comment: C: Log-transformed RNA-Seq data and linear regression
... I think log transformed count indeed maintains the original proportion, no? However for the purpose of the linear model, would log transformed count cause non-linearity? ...
written 8 weeks ago by CY270
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Comment: C: Log-transformed RNA-Seq data and linear regression
... Would log-transformed value violate the linearity assumption required for linear regression? Are independent variables and dependent variables still linear correlated after transformation? ...
written 8 weeks ago by CY270
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Any method to solve RNA-Seq's non-linearity problem for deconvoluting immune cell?
... I have been reading deconvolution method to separate RNA-Seq mixture into different immune cell. It seems that, like [this][1] and [this][2] discussion metioned, expression count from RNA-Seq data is not indenpende (non-linearly correlated) and this would result in poor accuracy of separation. How ...
deconvolution rna-seq written 8 weeks ago by CY270
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Comment: C: Why use LASSO / elastic net in survival regression?
... Yes. LASSO can get rid of some highly correlated variables and only keep one (sparser solution). But why do they make this judgement of using LASSO instead of regular Cox? Perhaps they think that their variables are redundant (highly correlated)? ...
written 11 weeks ago by CY270

Latest awards to CY

Popular Question 11 weeks ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 11 weeks ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Prophet 12 weeks ago, created a post with more than 20 followers. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 4 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 4 months ago, created a question with more than 1,000 views. For STAR genomeLoad issue
Popular Question 5 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Appreciated 7 months ago, created a post with more than 5 votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Student 9 months ago, asked a question with at least 3 up-votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Centurion 11 months ago, created 100 posts.
Supporter 14 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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