Showing : deg • reset
11
votes
15
replies
3.2k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
7.4 years ago baus87 • 0
6
votes
14
replies
3.4k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.8 years ago by ▴ 840 • written 6.8 years ago by ▴ 30
5
votes
13
replies
3.3k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
12
replies
2.3k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 20
3
votes
11
replies
1.8k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 19 months ago by 52k • written 19 months ago by • 0
0
votes
8
replies
1.4k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
votes
7
replies
1.7k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 20
1
vote
7
replies
2.3k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 2.5 years ago by 67k • written 2.5 years ago by • 0
1
vote
7
replies
2.2k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.8 years ago • updated 5.8 years ago SPbeginner • 0
4
votes
7
replies
4.8k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.7 years ago by ▴ 610 • written 7.7 years ago by ▴ 10
0
votes
6
replies
4.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 60
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.6 years ago reganhayward • 0
0
votes
6
replies
1.8k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
2.5 years ago • updated 2.4 years ago Weiqian ▴ 10
2
votes
6
replies
1.9k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
0
votes
5
replies
2.4k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
2.3 years ago • updated 2.2 years ago marinaw ▴ 20
1
vote
5
replies
2.0k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
4
votes
5
replies
1.7k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.9 years ago by 52k • written 4.9 years ago by ▴ 40
0
votes
5
replies
5.9k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 2.3 years ago by • 0 • written 2.9 years ago by • 0
2
votes
4
replies
1.9k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 20
0
votes
4
replies
1.5k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 5.2 years ago by ★ 13k • written 5.2 years ago by • 0
2
votes
4
replies
2.6k
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 6.4 years ago by • 0
3
votes
4
replies
2.1k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 6.1 years ago by 52k • written 6.1 years ago by ▴ 30
0
votes
4
replies
1.7k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 7.3 years ago by 52k • written 7.3 years ago by • 0
3
votes
4
replies
3.9k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
9.4 years ago • updated 9.3 years ago contato.carlosbau ▴ 10
0
votes
3
replies
2.1k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.8 years ago by 67k • written 6.8 years ago by • 0
3
votes
3
replies
7.5k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.9 years ago by ▴ 370 • written 9.9 years ago by • 0
2
votes
3
replies
1.6k
views
code for up-down-regulated Degs using R
limma deg
7.8 years ago nia ▴ 30
1
vote
3
replies
1.1k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
3
votes
3
replies
2.6k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
votes
3
replies
1.4k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
5
votes
2
replies
1.1k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 13 months ago by 52k • written 13 months ago by • 0
0
votes
2
replies
872
views
same results changing contrast function
deseq2 contrast DEG
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
votes
2
replies
1.5k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.8 years ago Shamim Sarhadi ▴ 20
2
votes
2
replies
1.5k
views
fdr score for degs
fdr deg
updated 7.7 years ago by ▴ 840 • written 7.7 years ago by ▴ 30
1
vote
2
replies
2.0k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 5.3 years ago by 52k • written 5.3 years ago by • 0
0
votes
2
replies
962
views
different designs for finding DEG by limma
limma DEG design
5.4 years ago amin.ghareyazi • 0
3
votes
2
replies
1.8k
views
DEG analysis by limma
DEG Limma
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
0
votes
1
reply
838
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 21 months ago by 52k • written 21 months ago by • 0
0
votes
1
reply
1.5k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 7.3 years ago by 52k • written 7.3 years ago by • 0
0
votes
1
reply
903
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 15 months ago by • 0 • written 3.5 years ago by • 0
1
vote
1
reply
916
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 30
0
votes
0
replies
991
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.7 years ago zroger499 • 0
0
votes
0
replies
1.9k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
6.9 years ago lawarde.ankita1 ▴ 30
1
vote
0
replies
2.4k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.8 years ago digrigor ▴ 10
0
votes
0
replies
534
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
0
votes
0
replies
1.6k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.7 years ago vharshavardhanan • 0
0
votes
0
replies
1.1k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
5.3 years ago chendianyu • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
Votes
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Awards • All
Commentator to Michael Love 43k
Popular Question to Gordon Smyth 52k
Popular Question to Jonathan ▴ 10
Popular Question to linouhao ▴ 20
Popular Question to spg • 0
Locations • All
United States, 6 minutes ago
United States, 26 minutes ago
United States, 43 minutes ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 730 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