Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DEG
•
reset
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
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
2
votes
3
replies
1.4k
views
code for up-down-regulated Degs using R
limma
deg
7.1 years ago
nia
▴ 30
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
Gordon Smyth
50k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
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
svlachavas
▴ 830 • written 6.1 years ago by
lawarde.ankita1
▴ 30
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
Biomed
• 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
Gordon Smyth
50k • written 5.4 years ago by
rproendo
▴ 20
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
Bernd Klaus
▴ 610 • written 7.0 years ago by
Maximilian
▴ 10
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
Ryan C. Thompson
★ 7.9k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
5
votes
2
replies
608
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 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 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
Pietro
▴ 40
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
Gordon Smyth
50k • written 11 months ago by
alexia.brunel
• 0
0
votes
8
replies
1.2k
views
Custom post-normalization counts from DESeq2
DEG
deseq2
Covariate
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
sum732
• 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
Michael Love
42k • written 4.8 years ago by
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
Michael Love
42k • written 4.7 years ago by
ecg1g15
▴ 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
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
b.nota
▴ 360 • written 9.2 years ago by
Yue Zhao
• 0
0
votes
3
replies
1.2k
views
DEG test for two closely related conditions with limma
limma
DEG
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Shamim Sarhadi
▴ 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
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
Steve Lianoglou
★ 13k • written 7.5 years ago by
Shamim Sarhadi
▴ 20
3
votes
2
replies
1.6k
views
DEG analysis by limma
DEG
Limma
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
Shamim Sarhadi
▴ 20
2
votes
2
replies
1.3k
views
fdr score for degs
fdr
deg
updated 7.1 years ago by
svlachavas
▴ 830 • written 7.1 years ago by
nia
▴ 30
0
votes
1
reply
1.4k
views
RNA-Seq DEG analysis questions
rnaseq
deg
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
mullin.yu
• 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
Gordon Smyth
50k • written 6.6 years ago by
JackieMe
• 0
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
James W. MacDonald
66k • written 6.1 years ago by
amy16
• 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
Michael Love
42k • written 5.2 years ago by
hermanapis
• 0
0
votes
1
reply
702
views
Multiple groups comparison using Linnorm
Linnorm
DEG
MultipleComparison
updated 7 months ago by
shunyip
• 0 • written 2.8 years ago by
awakumaya
• 0
0
votes
6
replies
3.5k
views
Performing simple pairwise comparisons in DESEQ2
edgeR
DEG
RNASeq
DESEQ2
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Raito92
▴ 60
0
votes
5
replies
4.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2
DEG
updated 20 months ago by
bioinfomagics
• 0 • written 2.3 years ago by
priya.dalvi
• 0
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
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.9 years ago
reganhayward
• 0
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 22 months ago by
James W. MacDonald
66k • written 22 months ago by
Diya
• 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
Gordon Smyth
50k • written 13 months ago by
Ankita
• 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
Gordon Smyth
50k • written 4.6 years ago by
kawess
• 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
James W. MacDonald
66k • written 4.6 years ago by
mjavad2012
• 0
0
votes
4
replies
1.3k
views
DESeq2 analysis with multiple factors
DESeq2
DEG
multiplefactors
deseq2
updated 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
yura.song
• 0
0
votes
2
replies
715
views
same results changing contrast function
deseq2
contrast
DEG
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
ire.ontiveros
• 0
1
vote
3
replies
853
views
DESeq2 - controlling for other variables
deseq2
DEG
covariate
study design
variables
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
Yonatan Amzaleg
• 0
3
votes
3
replies
2.1k
views
DEG analysis for Micro array affymetrix
DEG
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
sheikhbeigali
• 0
0
votes
0
replies
890
views
DEG among experimental and control group in MAST
MAST
DEG
batch effects
4.7 years ago
chendianyu
• 0
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
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
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 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
0
votes
2
replies
826
views
different designs for finding DEG by limma
limma
DEG
design
4.7 years ago
amin.ghareyazi
• 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
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
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
Germany,
just now
United States,
4 minutes ago
Taiwan,
5 minutes ago
EMBL Heidelberg,
20 minutes ago
Slovakia,
21 minutes ago
Traffic: 834 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