User: 1561775911

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15617759110
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Posts by 1561775911

<prev • 14 results • page 1 of 2 • next >
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a question about copy number alterations
... ![enter image description here][1] [1]: http://i.imgur.com/SeMuWzG.png this table is the supplementary table 9 of Copy number alterations across all tumors supplenmented in paper'Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors'. From line 2 to 1 ...
genome written 9 months ago by 15617759110 • updated 9 months ago by Biostar ♦♦ 20
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Comment: A: how to select gene mutation
... I have asked a Phd of genetics and he told me 1% was a custom ,while there is no standard for the mutation frequency threshold.That is why I ask if there is anyone who has more experience about this ...
written 10 months ago by 15617759110
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how to select gene mutation
... Hi,biostars, I have 200 patients with whole exome sequence and I want to build a multivariate Cox regression of overall survival with the gene mutations. First of all ,I should choose the mutational genes for the next modeling , while I don't know how to set threshold of mutation frequenc ...
cox regression mutation frequency written 11 months ago by 15617759110
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a question about gene mutation waterfall
... Hi,biostars, I am now ploting a waterfall figure of gene mutations(the function I used is waterfall function of GenVisR). When I tried to add the clinical data of PFS(Progressed Free Survival), I found that the clinical data should be categorical variable. Could anyone tell me how to add the PF ...
genome written 11 months ago by 15617759110
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Comment: C: edgeR - normalized counts from multiple datasets
... It works when I use the browser of chrome.You can share the experience of mine to others who does not use the browser of chrome ...
written 12 months ago by 15617759110
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Comment: A: edgeR - normalized counts from multiple datasets
... Hi, genomax, I want use the 'ADD REPLY', but when I click on it ,there is no response and I can only submit answer .What's more, 'ADD REPLY' button on my page is gray(I don't know which color is on your page ,but it seemed that it is invalid on my page).Could you please tell me the reason? #ps. brow ...
written 12 months ago by 15617759110
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Comment: A: edgeR - normalized counts from multiple datasets
... Hi,Kevin, I mean dge_TMM$counts is the same as the exprs which confused me.As I know,calcNormFactors(dge) is the process of TMM,but the dge_TMM$counts is not changed compared with the exprs ...
written 12 months ago by 15617759110
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Comment: A: edgeR - normalized counts from multiple datasets
... I have done the TMM and logCPM with code as follow: library(edgeR) dge<-DGEList(counts = as.matrix(exprs)) dge_TMM<-calcNormFactors(dge)#TMM logCPM <- cpm(dge_TMM, log=TRUE, prior.count=3)#log2 transformation But it confused me that when I compare the exprs matrix with the ...
written 12 months ago by 15617759110 • updated 12 months ago by Kevin Blighe44k
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Comment: A: edgeR - normalized counts from multiple datasets
... As I know, the methods of normalization for RNA-seq count include quantile normalization of limma-voom or edgeR.I can't confirm that these methods are suitable for RNA-seq count which will be used for the subsequent machine learning to find the predictors? ...
written 12 months ago by 15617759110
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Comment: A: What Are The Best Normalization Methods For Ngs Data
... Hi jack, I am doing similar works as you do before,and I also meet the problem of which methods to adopt for normalization of different kinds of RNA-seq count for a subsequent machine learning .And have you get the solution?Could you give me some advices? ...
written 12 months ago by 15617759110

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