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• Importing quantile normalized .txt file to limma for differential expression
  I am using limma package for identifying differential expression of affymetrix .CEL file. I used...
• RNAseq data normalization without differential expression
  Dear All, I have RNAseq counts for 400 human donors. This is a random sampling of human subjects...
• Is normalization in edgeR required for small RNA sequencing data?
  Dear All, I am PhD student, currently working on differential expression analysis of my smallRNA...
• edgeR
  Dear Bioconductor, I'm using EdgeR to find differentially expressed reads within 100bp windows. ...
• DEseq - treating input samples as replicates vs. rlog transformation
  We use DESeq2 package for differential expression quite a bit and I had a quick question regardin...
• affy, how to define the normalization method that works with my data
  hi to all bioconductor users! our goal is to find differentially expressed genes in cell line an...
• Limma then Annaffy?
  Hello all, Ive been searching the mail archives for about 2 hours without any luck on findi...
• effect of normalization on analysis of differential knockdown
  Hi, I am analysing the results from a drug sensitization siRNA screen and am trying to determine ...
• Normalization of array leads to decrease in number of differentially expressed genes
  Hi all, I performed normalization on my array data (I use qPCR array of 384 wells), and if I nor...
• DESeq questions
  Hi , I have RNA-seq count data for 30,400 genes across 6 conditions (3 replicates per condition)...
• Testing for no change in RNA-seq data?
  Hi all, So, we have several great packages for testing for evidence of differential expression u...
• TMM normalization of DESeq input data
  Hi, I have done differential expression analysis over RNA-seq data using both edgeR and DESeq. T...
• proper transformation for differential expression in normalized log expression data
  Dear R people, I want to do an analysis of differentially expressed genes between tumor and norm...
• differential expression methods
  Dear All, I have data from illumina experiments (one colora data) (48803 rows, 120 colones (40 ...
• DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
  Hello, My name is Kevin Lee, and I am a PhD candidate in Bioinformatics at Georgia Institute of ...
• [EDGER] Normalization issue
  Dear all, I am a master student in France, working on RNA-seq data. I am trying to go through a ...
• What RNA-Seq expression estimates to use for plotting to show voom/limma Differential expression
  HI Dr. Smyth, I am trying to find the appropriate mRNA expression level estimates to use for gen...
• Normalization quality assessment tools?
  Hi all, I've an experiment with almost 300 arrays, single channel (not Affymetrix, but some in-h...
• DEseq for paired samples
  Hi, I was looking for a method to identify differentially expressed genes using the paired tumor...
• Computing normalized counts for exons in edgeR
  I've done standard rna-seq differential expression analysis on a gene level using edgeR. For down...
• NA coefficients values for samples with all zeros
  I am trying to run a differential expression analysis for proteomics data using limma. The data h...
• HTqPCR Normalization
  Hi all, I use qPCR array of 384 wells and I normalize using d.norm. But I used different RNA inp...
• looking for advice on analysis methods
  Hi all, I am new to this field, and am looking for advice on what analysis methods I should use....