Showing : DEG • reset
3
votes
3
replies
6.9k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.2 years ago by ▴ 360 • written 9.2 years ago by • 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
0
votes
5
replies
4.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 20 months ago by • 0 • written 2.3 years ago by • 0
4
votes
7
replies
4.4k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 7.0 years ago by ▴ 610 • written 7.0 years ago by ▴ 10
0
votes
6
replies
3.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 60
3
votes
4
replies
3.4k
views
R Script for selecting differentially expressed genes
limma microarray affy deg
8.7 years ago contato.carlosbau ▴ 10
6
votes
14
replies
3.0k
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
11
votes
15
replies
2.8k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
6.8 years ago • updated 6.7 years ago baus87 • 0
5
votes
13
replies
2.7k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
2
votes
4
replies
2.4k
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 5.7 years ago by • 0
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.2 years ago digrigor ▴ 10
3
votes
3
replies
2.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
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 8.2 years ago by ▴ 20
1
vote
7
replies
1.9k
views
limma - Multi-level Experiments - time course data
limma limma voom rnaseq_analysis DEG
6.2 years ago • updated 5.2 years ago SPbeginner • 0
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error illumina DEG ballgown tuxedo
updated 6.1 years ago by 66k • written 6.1 years ago by • 0
1
vote
5
replies
1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
1
vote
4
replies
1.7k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 20
0
votes
5
replies
1.7k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
20 months ago • updated 18 months ago marinaw ▴ 20
2
votes
4
replies
1.7k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 22 months ago by 66k • written 22 months ago by • 0
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
6.3 years ago lawarde.ankita1 ▴ 30
3
votes
2
replies
1.6k
views
DEG analysis by limma
DEG Limma
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
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
4
replies
1.5k
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
2
votes
6
replies
1.5k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
4
votes
7
replies
1.5k
views
DEG analysis of chemo-sensitive vs resistance by limma
limma microarray DEG
updated 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 20
4
votes
5
replies
1.4k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 40
0
votes
6
replies
1.4k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
22 months ago • updated 21 months ago Weiqian ▴ 10
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
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown Stringtie DEG rnaseq
6.0 years ago vharshavardhanan • 0
0
votes
1
reply
1.4k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 6.7 years ago by 50k • written 6.7 years ago by • 0
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 4.6 years ago by ★ 13k • written 4.6 years ago by • 0
2
votes
2
replies
1.3k
views
fdr score for degs
fdr deg
updated 7.1 years ago by ▴ 830 • written 7.1 years ago by ▴ 30
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
0
votes
3
replies
1.2k
views
DEG test for two closely related conditions with limma
limma DEG
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
0
votes
8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
votes
0
replies
892
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.7 years ago chendianyu • 0
1
vote
3
replies
853
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
0
votes
2
replies
826
views
different designs for finding DEG by limma
limma DEG design
4.7 years ago amin.ghareyazi • 0
1
vote
1
reply
739
views
DeSeq RNASeq differential expression between region samples
R deseq2 DEG
updated 4.7 years ago by 42k • written 4.7 years ago by ▴ 20
0
votes
0
replies
723
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.0 years ago zroger499 • 0
0
votes
2
replies
715
views
same results changing contrast function
deseq2 contrast DEG
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
1
reply
702
views
Multiple groups comparison using Linnorm
Linnorm DEG MultipleComparison
updated 7 months ago by • 0 • written 2.8 years ago by • 0
0
votes
1
reply
630
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 13 months ago by 50k • written 13 months ago by • 0
5
votes
2
replies
608
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
0
replies
246
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
47 results • Page 1 of 1
Recent ...
Replies
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
United States, 8 minutes ago
Germany, 35 minutes ago
Switzerland, 36 minutes ago
United States, 39 minutes ago
San Diego, 40 minutes ago
Traffic: 643 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