sign of logfc in limma

How should the sign of the topTable from limma be interpreted? Which group is used as a reference to determine the sign of the logfc? I have only 2 groups in my factor. Thanks!

limma differential gene expression analysis

• 1,279 views • link

written 5.7 years ago by im •

Can you show the model matrix?

• 0 views • link

written 5.7 years ago by ATpoint

0 answers

No answers yet.

More posts like this

Interpretation of logFC in limma-voom contrasts
written 9 months ago by donan •

Hi everyone, I used limma-voom on RNA-seq data and I am trying to understand the results. I am using contrasts to compare group A versus …
How to divide participants into different groups based on genotype for several SNPs when some of th…
written 4.9 years ago by Mwangana •

Hi everyone, I have genotype data for 12 SNPs in over 100 healthy volunteers. I would like to divide the volunteers into three genotypic groups …
Explanation of Limma logFC calculation
written 6.8 years ago by John S. •

Hi guys, I have a doubt regarding the logFC calculation in limma. I searched for the answer in Biostars but I have not found anything …
RTqPCR Differential Expression with multivariate linnear models
written 7.7 years ago by Emilio Marmol

Hello everyone, So I have some data from RTqPCR experiment in different samples meassuring a number of genes (80-90). I have pre-processed de raw Ct …
[limma] LogFC interpretation
written 7.9 years ago by flappix •

Hi @ all, I have cel files from 2 groups, 3 replicates each group. I want to use limma for the differential gene expression analysis. …
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-…
written 7.9 years ago by BioLite •

Hi, all I'm a newbie, and I'm dealing with Agilent single channel microarray when I filtering DEGs using limma, I find all my results showing …
Meta output vs Toptable output
written 10.7 years ago by vn383 •

Hello, I am trying to compare values that I have generated from a meta output and Limma Toptable output in the form of a volcano …
Limma Contrast Question
written 12.0 years ago by pichai.raman •

Hello All, I'm using the Limma package to perform some microarray analysis. In the past I've typically compared 2 groups in contrasts such as "GroupA-GroupB". …
Design Matrix Microarray data analysis
written 12.0 years ago by jeevan92ultimate •

Hi, I'm analyzing a microarray data and stuck at the design matrix command. I have few samples, in which I divided them into two groups …
No Diffrently Expressed Mirna???
written 13.0 years ago by Sirus

<p>Hi guys, I know this question mqybe look silly but it is taking me a lot of time. I have downoaded some miRNA expression data …