User: archie

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archie90
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India
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Posts by archie

<prev • 86 results • page 1 of 9 • next >
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TCGA array expression and rnaseq expression batch correction
... Hi everyone In one of the article mentioned " Before starting the PDAC data analysis we first checked for possible batch effect in different types of data using Mbatch ". (Mishra et al 2019) here different data types refers to methylation, expression. 2) I found another script where batch effect ...
rnaseq tcga expression written 7 weeks ago by archie90
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Multi samples (Normal and Tumor) somatic SNPs identification
... Hi everyone I have bam files of multiples normal and tumor samples. For the efficient SNPs prediction, Its recommended to have merged multi sample vcf file. These are steps I followed 1. Mapping of all T and N samples to get multi samples bam file ( Tumor 20 Bam files : Normal 20 Bam files) 2. ...
vcf gatk snp mutlisamplevcf whole-exom written 10 weeks ago by archie90
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multi sample vcf to data matrix
... Hi everyone I have almost 50 VCF files consisting of information of somatic and germline SNPs. I need to convert this data from vcf to matrix format as given below : sample1 samples2 Gene1 0 1 Gene2 1 0 Gene3 1 ...
vcf gatk snp written 10 weeks ago by archie90 • updated 10 weeks ago by ATpoint26k
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Comment: C: TCGA survival data classification
... Thanks alot Kevin. It helped alot. ...
written 10 weeks ago by archie90
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TCGA survival data classification
... Hello everyone, I am working on one of the Ovarian cancer TCGA clinical data . I would like to classify patients into two classes based on the survival. I took the column days to death (short : less than three years survival (365*3) and long : > 365*3 : greater than three year survival and cla ...
tcga survival written 11 weeks ago by archie90 • updated 10 weeks ago by Kevin Blighe51k
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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 8 months ago by archie90
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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 8 months ago by archie90
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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 8 months ago by archie90 • updated 8 months ago by WouterDeCoster42k
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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 10 months ago by archie90 • updated 8 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 10 months ago by archie90

Latest awards to archie

Popular Question 6 weeks 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 Error while running discoSNP
Popular Question 3 months ago, created a question with more than 1,000 views. For Markduplicates in RNASEQ
Popular Question 4 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 4 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 7 months ago, created a question with more than 1,000 views. For rRNA in human
Scholar 8 months ago, created an answer that has been accepted. For C: Error of Netics : Multi omics intergration tool
Popular Question 10 months ago, created a question with more than 1,000 views. For rRNA in human

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