User: archie

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archie70
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Posts by archie

<prev • 81 results • page 1 of 9 • next >
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Answer: A: Merging variant calls of whole exome and RNA-seq
... Hi , You can go through this paper https://github.com/aradenbaugh/radia where authors mentioned use of DNA and RNA snps but it is tumor specific. I hope , this can work for you. ...
written 4 months ago by archie70
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Answer: C: Error of Netics : Multi omics intergration tool
... It worked for me. I downloaded fdr function from https://brainder.org/2011/09/05/fdr-corrected-fdr-adjusted-p-values/ I missed this information earlier. Test run is working now. Thanks ...
written 4 months ago by archie70
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Error of Netics : Multi omics intergration tool
... Hello everyone, I am running Netics code to prioritize genes in my project. Basically, I am working on PDAC cancer . I have transcriptome and mutation data. I am trying to run 'NETICS' code available at https://github.com/cbg-ethz/netics. As a very first step, I am trying to run test data given ...
multi omics integration netics written 4 months ago by archie70 • updated 4 months ago by WouterDeCoster40k
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Survival analysis based on gene expression
... Hello everyone I performed the gene expression based survival analysis and selected genes (1700 genes) with Log-Rank test p value < 0.05. I have list of LogRank" "HR" "HRlower" "HRupper" associated to each gene. But , I want to classify genelist into further two gene lists: high expression patte ...
gene expression survival written 6 months ago by archie70 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: ConsensusClusterPlus for small sample
... Hi Ahill Thanks for your valuable answer. I will go with MAD approach for variable selection. As z score were predicted sample Wise. First, I will start with normalised intensities and will try to get results. Then will try get subgrouping with z score and later on will see how common results are ...
written 6 months ago by archie70
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ConsensusClusterPlus for small sample
... Hello everyone I want to identify subgroups in one of cancer dataset. Before using it, I have few questions : 1) What are minimum sample size required to run ConsensusClusterPlus . I have data of 19 samples . Shall I use it for clustering or I should go for other method (eg PCA). 2) While going ...
consensusclusterplus written 6 months ago by archie70 • updated 4 months ago by chris86290
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cytoscape subnetwork from WGCNA based modules
... Hello I have identified modules linked to some traits of interest in our study. All modules were imported in cytoscape. As next step, I want to predict subnetwork using TieDie ( one of the cytoscape App). One of the network consist of 102 edges and 306 nodes. After running, TieDie on that netwo ...
tiedie subnetwork cytoscape written 10 months ago by archie70 • updated 10 months ago by RamRS22k
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Comment: C: TCGA SNP data
... Hello My problem is during conversion from maf to vcf, loosing many SNP sites or data information via by use of maf2vcf.pl, which is not normal. I tried to fixed it, but not succeeded. Now I will follow your suggestion and will create custom PED and MAP. I already created .fam for dataset. Thank ...
written 11 months ago by archie70
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Comment: C: TCGA SNP data
... Dear kevin In one of project , converted vcf to plink and performed downstream analysis. Therefore I thought of following the same strategy for TCGA as well . For "custom PED and MAP", ya i will check. Thanks for your suggestion Archana ...
written 11 months ago by archie70
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TCGA SNP data
... Dear all In one of my project, I have to use the SNPs from TCGA (PAAD) and convert them into plink format and use for further analysis. There are many issues , that I faced 1. I was not able to capture all the sites while convering .maf to .vcf. Although I used exactly same genome version as men ...
maf2vcf snps paad tcga written 11 months ago by archie70 • updated 11 months ago by Kevin Blighe46k

Latest awards to archie

Popular Question 1 day ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 28 days ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 3 months ago, created a question with more than 1,000 views. For rRNA in human
Scholar 4 months ago, created an answer that has been accepted. For C: Error of Netics : Multi omics intergration tool
Popular Question 6 months ago, created a question with more than 1,000 views. For rRNA in human

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