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 days 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 6 days 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 11 days ago by archie70 • updated 6 days ago by WouterDeCoster37k
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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 7 weeks ago by archie70 • updated 23 days 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 10 weeks 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 10 weeks ago by archie70 • updated 10 weeks ago by Ahill1.4k
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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 6 months ago by archie70 • updated 6 months ago by RamRS20k
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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 7 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 7 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 7 months ago by archie70 • updated 7 months ago by Kevin Blighe39k

Latest awards to archie

Scholar 6 days ago, created an answer that has been accepted. For C: Error of Netics : Multi omics intergration tool
Popular Question 9 weeks ago, created a question with more than 1,000 views. For rRNA in human

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