Showing : deg • reset
11
votes
15
replies
3.9k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
8.3 years ago baus87 • 0
3
votes
4
replies
4.5k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
10.3 years ago • updated 10.2 years ago contato.carlosbau ▴ 10
2
votes
3
replies
1.8k
views
code for up-down-regulated Degs using R
limma deg
8.7 years ago nia ▴ 30
2
votes
4
replies
2.2k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 20
3
votes
11
replies
2.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
votes
4
replies
3.0k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma toptable deg logfc
written 7.3 years ago by • 0
3
votes
4
replies
2.6k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 30
4
votes
7
replies
5.4k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 8.6 years ago by ▴ 610 • written 8.6 years ago by ▴ 10
5
votes
12
replies
3.0k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 20
6
votes
14
replies
4.1k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.7 years ago by ▴ 840 • written 7.7 years ago by ▴ 30
4
votes
5
replies
2.1k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 5.8 years ago by 53k • written 5.9 years ago by ▴ 40
5
votes
2
replies
1.6k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
0
votes
8
replies
1.7k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
5
votes
13
replies
4.1k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
1
vote
1
reply
1.2k
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
2
votes
4
replies
2.7k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
6 months ago Maziya • 0
3
votes
3
replies
8.1k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.8 years ago by ▴ 370 • written 10.8 years ago by • 0
0
votes
3
replies
1.7k
views
DEG test for two closely related conditions with limma
limma DEG
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 20
0
votes
2
replies
1.7k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
9.7 years ago Shamim Sarhadi ▴ 20
4
votes
7
replies
2.1k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 9.0 years ago by ★ 13k • written 9.0 years ago by ▴ 20
3
votes
2
replies
2.1k
views
DEG analysis by limma
DEG Limma
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 20
2
votes
2
replies
1.8k
views
fdr score for degs
fdr deg
updated 8.6 years ago by ▴ 840 • written 8.6 years ago by ▴ 30
0
votes
1
reply
1.7k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
0
votes
4
replies
2.0k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
1
vote
7
replies
2.6k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
7.7 years ago • updated 6.8 years ago SPbeginner • 0
0
votes
3
replies
2.4k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
1
vote
5
replies
2.4k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
votes
6
replies
5.4k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 60
0
votes
5
replies
7.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 3.2 years ago by • 0 • written 3.8 years ago by • 0
0
votes
6
replies
2.3k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.4 years ago Weiqian ▴ 10
2
votes
6
replies
6.1k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago reganhayward • 0
0
votes
5
replies
3.2k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
3.2 years ago • updated 3.1 years ago marinaw ▴ 20
1
vote
7
replies
2.9k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
votes
1
reply
1.1k
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
vote
2
replies
2.5k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
2
votes
6
replies
2.2k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
votes
4
replies
1.8k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
0
votes
2
replies
1.1k
views
same results changing contrast function
deseq2 contrast DEG
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
3
replies
1.4k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
votes
3
replies
3.3k
views
DEG analysis for Micro array affymetrix
DEG
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
votes
1
reply
1.2k
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 2.2 years ago by • 0 • written 4.4 years ago by • 0
0
votes
0
replies
1.3k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
6.2 years ago chendianyu • 0
0
votes
0
replies
1.3k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.6 years ago zroger499 • 0
1
vote
0
replies
2.8k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.7 years ago digrigor ▴ 10
0
votes
0
replies
2.2k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
7.8 years ago lawarde.ankita1 ▴ 30
0
votes
0
replies
1.8k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
7.6 years ago vharshavardhanan • 0
0
votes
2
replies
1.2k
views
different designs for finding DEG by limma
limma DEG design
6.3 years ago amin.ghareyazi • 0
0
votes
0
replies
770
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
48 results • Page 1 of 1
Recent ...
Replies
Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Locations • All
European Union, 5 minutes ago
United States, 16 minutes ago
United States, 29 minutes ago
United States, 1 hour ago
The city by the bay, 1 hour ago
Traffic: 640 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6