Similar posts • Search »

• Can NanoString data be analyzed using DESeq2?
  Hello, I am trying to analyze differential expressed genes using NanoString data. There are a num...
• Application of RUV to a small Nanostring dataset
  Subject: Application of RUV to a small Nanostring dataset Dear Forum, I will soon be analyzing ...
• lmFit very slow if there are missing values
  Having only a single missing value slows lmFit down by over an order of magnitude: library("...
• The number of the counts columns uploaded to the Deseq2 affected the number of reported DEG
  I has just started using Deseq2 to discovery deferentially expressed genes (DEGs). In my data, ...
• Suggestions for avoiding False Positives while identifying differentially expressed genes with more than 3 samples per group
  Hi, I have RNA seq data with the samples defined as follows: **ID level stability type*...
• Multifactor design in DESeq2 - infection effect over time on three different plant cultivars
  Hi, I am running *DESeq2* to get DEGs from experiment below. The experimental design I am workin...
• TopTable vs DecideTests: can I just extract DEs with decidetest rowsums !=0?
  Hi everyone, I am looking for critique on the methods I've used to find DEGs in my data. I ini...
• Heatmap of selected genes
  Hi all! I analyzed my RNAseq data with DESeq2 and I obtained a nice unsupervised Heatmap with my ...
• limma for getting DEGs from my own input matrix
  Hi I have normalized RNAseq data for treatment and control of a particular cell line. The matrix ...
• Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
  Dear all, If I understand correctly, TMM-normalisation has two assumptions: 1. Most genes are n...
• Meta_analysis of different platforms of microarray data
  Hi Dears… In a meta-analysis study, I am trying to find DEGs from different individual studies wi...
• DESeq2: thousands of NA for pvalues?
  I have a RNA seq data which I am trying to identify DEGs. Dataset contains three sets of Untreate...
• alpha and p-adjust value
  Hello; I am using DESeq2 for DEG discovery, however I found changes in p-adjust value depending ...
• Limma Design matrix for time series+treatment+batch effect
  dear all, I'm trying to get a DEG analysis of a microarray data. I have 9 placebo and 9 treated...
• Any recommended workflow for incrementally selecting top ranked genes by using mRMR feature selection?
  Hi: I am using Affymetrix microarray gene expression data, and I am trying to do feature selecti...
• Identifying cell line-independent DEG in a time series (DESeq2)
  Hello there. I would like to identify the cell line-independent differentially expressed genes i...