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• DESeq2 result contrast
  I have three genotypes (I,II,III) and conditions (infected,mock) When i do the DESeq2 analysis ...
• DESeq2 model design
  I have a data , like this Genotype condition time A ...
• DESeq2 to analyse OTU differential abundance
  Hi, I am currently trying to use DeSeq2 to look at  differential abundance in my OTU data. My pr...
• DESeq2: Differential gene expression
  Hi, I am working on RNA-Seq data for Arabidopsis plant. I have samples from 4 genotypes (A, B, C,...
• DGE Analysis between 3 conditions
  Hi, I have datasets for 3 different conditions`["WT", "KO", "KO1"]` (each with 3 replicates). [a...
• Deseq2 question of a single factor with 3 levels
  Hi, I am a RNA-seq beginner. Recently, I have a RNA-seq project. There is one factor with 3 level...
• DESeq2: (1) Comparing multiple groups using a for loop & (2) normalization of time series data with housekeeping gene counts
  Hi Everyone: I am trying to analyze a set of RNAseq data using DESeq2 to do a GO enrichment anal...
• Error in running DESeqDataSetFromTximport
  Hello, I am facing an error while running DESeqDatasetFromTximort after StringTie quantification...
• DESeq : base mean value are same for all genes in all the three combinations in compare all levels design
  My RNA-seq dataset consist of Resis_treated (1st day, 3rd day and 7th day) samples taken under 3 ...
• Deseq2 with one factor and multiple levels
  Dear all, I'm dealing with and RNA-seq experiment with a total of 11 different conditions. I'd...
• DESeq2 very high p-values and padj
  I'm comparing a control vs Treatment A and control vs.Treatment B with DESeq2 though the pvalues ...
• Strange MA-plot using DESeq2
  Hello, I am using DESeq2 to perform some differential expression analysis between 3 levels of a ...
• Deseq2: time series in 1 condition. Error in nbinomLRT(object, full = full, reduced = reduced, quiet = quiet
  I am using DEseq2 to do differential analysis from RNA-seq data across 4 developmental stages, ea...
• error in getting results from DESeq2
  Dear all, I am trying to run DESeq2 to get the list of differential expressed miRNAs between 330 ...
• multi-factor Deseq LRT test analysis
  Hi All, I need help to resolve the design to get differentially expressed gene with deseq2. I ha...
• DESeq2 4 group comparison
  I want to compare the DEG expression levels in WT(Wild Type) and three mutants(mutantA, mutantB, ...
• error related to coefficients while running DESeq2 in R
  Hi, I am kind of new in R so I apologize if I dont give required information to my question. I ha...
• SVA + DESEQ2 : Looking for batcheffect in RNA-SEQ
  I have set a model where I look to different conditions adjusting on a potential batch effect.([s...
• DESeq2 compare all levels using wald and lrt test
  I am currently working in plant pathogen interaction and is trying to make a gene co-expression n...
• DESeq2 doesn't compare the right ctrl vs treatment?
  We have a very simple experiment, 1 control (C) and 3 independent treatments (T, B, A). So techni...
• comparision pairwise samples with DESeq2
  Hello I need your help to resolve this problem with DESeq2 because It's my first experience with...
• Deseq2 multiple comarison
  I m using deseq2 for my samples such as Wild type[untreated] , and two treated condition [with vi...
• DESeq2 results interpretation
  how can i see the expression level? and which result shows if a gene is differentially expressed ...