User: CY

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CY270
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270
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https://www.dna-ghost....
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Posts by CY

<prev • 169 results • page 1 of 17 • next >
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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 1 day ago by CY270
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Comment: C: Differential gene expession analysis in cell populations of mixed tumor and norm
... I came across [this article][1] stating TPM from salmon and kalisto may yield better linear result. Is this a way to solve the problem? [1]: https://www.rna-seqblog.com/comprehensive-evaluation-of-rna-seq-quantification-methods-for-linearity/ ...
written 1 day 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 19 days ago by CY270
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Why use LASSO / elastic net in survival regression?
... We usually use cox model for survival analysis. However, some papers (PMID: 29628290) used LASSO / elastic net regularized survival regression. What is the reason using that? Is it because researchers think some of variables are not indenpendent (highly correlated)? ...
lasso survival analysis written 19 days ago by CY270 • updated 19 days ago by Jean-Karim Heriche17k
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Any tools for co-mutation analysis just like WGCNA on co-expression analysis
... I know that WGCNA is widely used in co-expression analysis. I have a number of tumor samples and try to find significantly co-occurrent mutation across samples. My assumption is that certain combination of mutations is pathological. I am not sure if WGCNA can be used for co-mutation. Is there any m ...
expression mutation written 22 days ago by CY270
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Forum: Have TCGA yielded expected research value yet?
... TCGA project has been finished for a whole and lots of research has used to generate molecular characteristic of tumors. As the most ambitious and widely used data source in related topic so far, I would say it has already yielded significant research value. But if we compare what has been yielded ...
forum tcga written 23 days ago by CY270
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Comment: C: Log-transformed RNA-Seq data and linear regression
... Interesting. I have never thought of that. Is it (expression comparison of log-normalized count reflects the expression difference on real world scale) a widely accepted thoughts? ...
written 29 days ago by CY270
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Comment: C: Can remote, but same type, tissue be used as RNA-Seq normal control for tumor st
... Thanks for the comments. I am aware of batch effect in RNA-Seq analysis. We will extract samples in the same batch. My concern is the use of rmote normal tissue as control instead of adjencent tissue which is not accessible for some reason. I imagine that would be all right since the same tissue w ...
written 29 days ago by CY270
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Can remote, but same type, tissue be used as RNA-Seq normal control for tumor study?
... Usually, adjacent tissue is used as RNA-Seq normal control. However, Adjacent tissue is not accessible in some case. Can I use remove, but same type, tissue instead? Beside, adjencent tissue in many cases is not typical 'normal' tissue. It may contain certain degree of tumor cells and immune cells ...
rna-seq written 4 weeks ago by CY270 • updated 4 weeks ago by kristoffer.vittingseerup1.0k
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Comment: C: Why NMF for mutation signature analysis
... Thanks for explaining. I had some digging. Some methods explain the use of sparse solution is that most mutagens are highly specific in the type of damage they cause, and therefore the majority of somatic mutational signatures are sparse. ...
written 4 weeks ago by CY270

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Popular Question 16 days ago, created a question with more than 1,000 views. For what cause poly-G from NextSeq
Popular Question 16 days ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Prophet 26 days ago, created a post with more than 20 followers. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For STAR genomeLoad issue
Popular Question 3 months ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Appreciated 5 months ago, created a post with more than 5 votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For why PCA for RNA-Seq but tSNE for scRNA-seq?
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Popular Question 13 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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