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• gene set enrichment analysis for continuous phenotype
  I want to do gene set enrichment analysis but outcome (phenotype) of the data is continuous. Is t...
• correlating microarray data to continuous phenotype variable
  Typically when working on microarray data I work in log2 space (e.g. when calculating DE or corre...
• how to test for significant phenotype enrichment in phylogenetic tree clusters
  I have a phylogenetic tree with strains grouped into specific clusters/lineages. Strains are assi...
• Adjusting binary phenotype (case/ctrl) for Polygenic Risk Score (PRS)
  Hi everyone, I am a little confusing of how to adjust binary phenotype for polygenic risk score...
• SNPTEST:number of samples below limit
  Hi, I have recently started doing GWAS and I chose to do it with SNPTEST. I would appreciate if ...
• How to use an ordinal or discrete phenotype in plink?
  I want to run an association using plink.  I know that you can use data that is continuous and da...
• Rare variant meta-analyzing tests
  Hi all, I have 5 different (dosage VCF files, with both continuous and binary phenotypes) datase...
• Plink input, phenotypes and multiple testing
  I have final reports from Illumina beadchips. The reports only include Allele 1 TOP and Allele 2 ...
• Measure Significance Of Genes Associated With Multiple Phenotypes
  I have a dataset of gene-phenotype association in this format. I am looking at some combination ...
• Phenotype from plink fam file in gcta
  My question is about specifying phenotype file in GCTA analysis. My phenotype data is in my .fam ...
• Non parametric quantitative genome wide association tests
  I am running a Genome Wide Association test, using a quantitative phenotype. This phenotype can h...
• Gene Set Enrichment Analysis using Variant Density instead of Expression levels?
  Hi, I have a list of genes, along with their variant densities. I can decide which variants to us...
• Possible methodology-R package for simulating a microarray dataset with both gene and clinical continuous features
  Dear Community, through R and based on a microarray gene expression dataset (60 samples in total...
• Exome sequencing and association
  Hello all, I have some fundamental question regarding the association of a phenotype (drug toxic...
• GSEA Phenotype Table Input
  Hello All, I am trying use GSEA for gene enrichment analysis, and I was wondering about the phen...