Showing : DEG • reset
0
votes
0
replies
204
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 weeks ago Abril • 0
5
votes
2
replies
531
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
1
reply
677
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 6 months ago by • 0 • written 2.7 years ago by • 0
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
votes
1
reply
594
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
5
replies
1.6k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
19 months ago • updated 17 months ago marinaw ▴ 20
0
votes
6
replies
1.4k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
21 months ago • updated 20 months ago Weiqian ▴ 10
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 21 months ago by 65k • written 21 months ago by • 0
0
votes
0
replies
697
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
0
votes
5
replies
4.2k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 19 months ago by • 0 • written 2.2 years ago by • 0
0
votes
6
replies
3.4k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.2 years ago by 41k • written 2.2 years ago by ▴ 60
2
votes
4
replies
2.3k
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 5.6 years ago by • 0
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago • updated 2.8 years ago reganhayward • 0
3
votes
3
replies
2.0k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
1
vote
3
replies
827
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
4
votes
5
replies
1.4k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 40
0
votes
2
replies
701
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.5 years ago by ★ 13k • written 4.5 years ago by • 0
2
votes
6
replies
1.4k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
1
vote
2
replies
1.5k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 4.6 years ago by 50k • written 4.6 years ago by • 0
0
votes
0
replies
871
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
0
votes
2
replies
806
views
different designs for finding DEG by limma
limma DEG design
4.6 years ago amin.ghareyazi • 0
1
vote
1
reply
720
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 20
5
votes
13
replies
2.7k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
8
replies
1.1k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
1
vote
7
replies
1.9k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.1 years ago • updated 5.1 years ago SPbeginner • 0
1
vote
5
replies
1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
1
vote
4
replies
1.7k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.0 years ago by 65k • written 6.1 years ago by • 0
6
votes
14
replies
2.9k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.1 years ago by ▴ 830 • written 6.1 years ago by ▴ 30
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.1 years ago digrigor ▴ 10
0
votes
0
replies
1.6k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
6.2 years ago lawarde.ankita1 ▴ 30
0
votes
4
replies
1.5k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
11
votes
15
replies
2.7k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.7 years ago baus87 • 0
4
votes
7
replies
4.3k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 6.9 years ago by ▴ 610 • written 6.9 years ago by ▴ 10
2
votes
2
replies
1.3k
views
fdr score for degs
fdr deg
updated 7.0 years ago by ▴ 830 • written 7.0 years ago by ▴ 30
2
votes
3
replies
1.4k
views
code for up-down-regulated Degs using R
limma deg
7.1 years ago nia ▴ 30
3
votes
2
replies
1.5k
views
DEG analysis by limma
DEG Limma
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
4
votes
7
replies
1.4k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 7.4 years ago by ★ 13k • written 7.4 years ago by ▴ 20
0
votes
2
replies
1.3k
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma taptable DEG
8.1 years ago Shamim Sarhadi ▴ 20
5
votes
12
replies
1.9k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 8.1 years ago by ★ 7.9k • written 8.1 years ago by ▴ 20
0
votes
3
replies
1.2k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
2
votes
4
replies
1.6k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.1 years ago by 50k • written 8.1 years ago by ▴ 20
3
votes
4
replies
3.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.6 years ago contato.carlosbau ▴ 10
3
votes
3
replies
6.8k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.1 years ago by ▴ 360 • written 9.1 years ago by • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
WEHI, Melbourne, Australia, 1 minute ago
EMBL Heidelberg, 14 minutes ago
France, 17 minutes ago
France, 17 minutes ago
United States, 20 minutes ago
Traffic: 1084 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