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
0
votes
6
replies
276
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq
DEG
DESeq2
19 days ago • updated 11 days ago
Weiqian
• 0
1
vote
7
replies
232
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 4 weeks ago by
James W. MacDonald
60k • written 4 weeks ago by
Diya
• 0
0
votes
0
replies
113
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
3 months ago
zroger499
• 0
0
votes
4
replies
667
views
DESeq2/Differential expression analysis without replicates
DESeq2
DEG
5 months ago
priya.dalvi
• 0
0
votes
6
replies
634
views
Performing simple pairwise comparisons in DESEQ2
edgeR
DEG
RNASeq
DESEQ2
updated 6 months ago by
Michael Love
37k • written 6 months ago by
Raito92
▴ 60
0
votes
0
replies
190
views
Multiple groups comparison using Linnorm
Linnorm
DEG
MultipleComparison
12 months ago
awakumaya
• 0
2
votes
4
replies
1.6k
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 3.9 years ago by
Biomed
• 0
2
votes
6
replies
1.4k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
14 months ago
reganhayward
• 0
3
votes
3
replies
642
views
DEG analysis for Micro array affymetrix
DEG
updated 2.3 years ago by
Kevin Blighe
3.6k • written 2.3 years ago by
sheikhbeigali
• 0
1
vote
3
replies
353
views
DESeq2 - controlling for other variables
deseq2
DEG
covariate
study design
variables
updated 2.5 years ago by
Michael Love
37k • written 2.5 years ago by
Yonatan Amzaleg
• 0
4
votes
5
replies
632
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 2.5 years ago by
Gordon Smyth
46k • written 2.5 years ago by
Pietro
▴ 30
0
votes
2
replies
322
views
same results changing contrast function
deseq2
contrast
DEG
updated 2.8 years ago by
Michael Love
37k • written 2.8 years ago by
ire.ontiveros
• 0
0
votes
4
replies
685
views
DESeq2 analysis with multiple factors
DESeq2
DEG
multiplefactors
deseq2
updated 2.8 years ago by
Steve Lianoglou
13k • written 2.8 years ago by
yura.song
• 0
2
votes
6
replies
575
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR
DEG
updated 2.8 years ago by
James W. MacDonald
60k • written 2.8 years ago by
mjavad2012
• 0
1
vote
2
replies
715
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma
microarray
time series
DEG
paired
updated 2.9 years ago by
Gordon Smyth
46k • written 2.9 years ago by
kawess
• 0
0
votes
0
replies
406
views
DEG among experimental and control group in MAST
MAST
DEG
batch effects
2.9 years ago
chendianyu
• 0
0
votes
2
replies
409
views
different designs for finding DEG by limma
limma
DEG
design
3.0 years ago
amin.ghareyazi
• 0
1
vote
1
reply
313
views
DeSeq RNASeq differential expression between region samples
R
deseq2
DEG
updated 3.0 years ago by
Michael Love
37k • written 3.0 years ago by
ecg1g15
• 0
5
votes
13
replies
1.2k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2
DEG
ANOVA
Batch effect
Comparison
updated 3.0 years ago by
Michael Love
37k • written 3.0 years ago by
amin.ghareyazi
• 0
0
votes
8
replies
500
views
Custom post-normalization counts from DESeq2
DEG
deseq2
Covariate
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
sum732
• 0
1
vote
7
replies
1.1k
views
limma - Multi-level Experiments - time course data
limma
limma voom
rnaseq_analysis
DEG
4.4 years ago • updated 3.4 years ago
SPbeginner
• 0
1
vote
5
replies
888
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2
DE
DEG
updated 3.5 years ago by
Michael Love
37k • written 3.5 years ago by
hermanapis
• 0
1
vote
4
replies
939
views
Implications of TMM Normalization and Possible Alternatives
edger
TMM
DEG
normalization
updated 3.6 years ago by
Gordon Smyth
46k • written 3.6 years ago by
rproendo
▴ 20
0
votes
0
replies
797
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
4.3 years ago
vharshavardhanan
• 0
0
votes
3
replies
1.2k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 4.4 years ago by
James W. MacDonald
60k • written 4.4 years ago by
amy16
• 0
6
votes
14
replies
1.8k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA
FireBrowse
limma
DEG
updated 4.4 years ago by
svlachavas
▴ 800 • written 4.4 years ago by
lawarde.ankita1
▴ 20
1
vote
0
replies
1.2k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo
gene ontology
pathway analysis
rnaseq
DEG
4.4 years ago
digrigor
▴ 10
0
votes
0
replies
1.1k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
4.5 years ago
lawarde.ankita1
▴ 20
0
votes
4
replies
771
views
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma
deg
microarray
updated 4.8 years ago by
Gordon Smyth
46k • written 4.8 years ago by
JackieMe
• 0
0
votes
1
reply
841
views
RNA-Seq DEG analysis questions
rnaseq
deg
updated 4.9 years ago by
Gordon Smyth
46k • written 4.9 years ago by
mullin.yu
• 0
11
votes
15
replies
1.8k
views
edgeR - MDS Plot for Count Data
edger
DEG
mds
plot
5.0 years ago
baus87
• 0
4
votes
7
replies
2.9k
views
Alternative packages to limma for analysis of microarray datasets
limma
microarray
deg
updated 5.2 years ago by
Bernd Klaus
▴ 600 • written 5.2 years ago by
Maximilian
▴ 10
2
votes
2
replies
786
views
fdr score for degs
fdr
deg
updated 5.3 years ago by
svlachavas
▴ 800 • written 5.3 years ago by
nia
▴ 30
2
votes
3
replies
904
views
code for up-down-regulated Degs using R
limma
deg
5.4 years ago
nia
▴ 30
3
votes
2
replies
995
views
DEG analysis by limma
DEG
Limma
updated 5.7 years ago by
Aaron Lun
★ 27k • written 5.7 years ago by
Shamim Sarhadi
▴ 20
4
votes
7
replies
859
views
DEG analysis of chemo-sensitive vs resistance by limma
limma
microarray
DEG
updated 5.7 years ago by
Steve Lianoglou
13k • written 5.7 years ago by
Shamim Sarhadi
▴ 20
0
votes
2
replies
776
views
Comparison between two outputs of limmas toptable function from filtered and unfiltered dataset
limma
taptable
DEG
6.4 years ago
Shamim Sarhadi
▴ 20
5
votes
12
replies
1.2k
views
Filtering before the linear modelling and empirical bayes steps
DEG
Limma
Filtering
updated 6.4 years ago by
Ryan C. Thompson
7.8k • written 6.4 years ago by
Shamim Sarhadi
▴ 20
0
votes
3
replies
809
views
DEG test for two closely related conditions with limma
limma
DEG
updated 6.4 years ago by
Aaron Lun
★ 27k • written 6.4 years ago by
Shamim Sarhadi
▴ 20
2
votes
4
replies
1.0k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA
DEG
updated 6.4 years ago by
Gordon Smyth
46k • written 6.4 years ago by
Shamim Sarhadi
▴ 20
3
votes
4
replies
2.6k
views
R Script for selecting differentially expressed genes
limma
microarray
affy
deg
6.9 years ago
contato.carlosbau
▴ 10
3
votes
3
replies
5.4k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg
rna-seq
rpkm
updated 7.4 years ago by
b.nota
▴ 360 • written 7.4 years ago by
Yue Zhao
• 0
42 results • Page
1 of 1
Recent ...
Replies
Comment: Retrieve gene summary start/end in biomart query
by
rbenel
▴ 20
Hi Mike, I have tried the query without the transcript, and I believe there are cases where I will receive unique transcript start/end si…
Comment: MMDiff2 memory issues
by
e.iich
• 0
running against a similar issue. Have you found any solutions?
Answer: mapToAlignments_issue
by
Hervé Pagès
15k
> I would expect in case of reverse alignment lifted ranges to correspond to position 91-100 of the query sequence. Nope. Local coordinate…
Answer: Problem related to `biomaRt::getBM()` during `R CMD check` execution
by
James W. MacDonald
60k
Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?
Comment: OPLS-DA: confidence interval for accuracy metric
by
Eddie
• 0
Worked well under pROC. Thank you
Votes
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
Awards
• All
Popular Question
to
e.iich
• 0
Popular Question
to
Gordon Smyth
46k
Popular Question
to
gv
▴ 40
Scholar
to
Hervé Pagès
15k
Popular Question
to
ta_awwad
▴ 10
Locations
• All
Iran,
13 minutes ago
Germany,
26 minutes ago
China,
30 minutes ago
Switzerland,
41 minutes ago
Israel,
52 minutes ago
Traffic: 351 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