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DEGseq
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3
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396
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
written 4 months ago by
Jonathan
• 0
0
votes
9
replies
1.8k
views
limma fo continous variables
limma
DEGseq
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
mia
• 0
0
votes
1
reply
862
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 19 months ago by
ATpoint
★ 4.8k • written 19 months ago by
sybyun419
• 0
0
votes
2
replies
824
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 21 months ago by
Gordon Smyth
52k • written 21 months ago by
Shaimaa Gamal
• 0
2
votes
5
replies
1.6k
views
Create the design matrix
DEGseq
edgeR
RNASeq
2.3 years ago
Mohammad
• 0
0
votes
0
replies
1.2k
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
2.4 years ago
Rob
• 0
0
votes
2
replies
1.1k
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
CP
• 0
0
votes
2
replies
1.2k
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 2.7 years ago by
swbarnes2
★ 1.4k • written 2.8 years ago by
ac.mainul.mmb
• 0
1
vote
4
replies
1.3k
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 2.9 years ago by
Kevin Blighe
★ 4.0k • written 2.9 years ago by
beslinail
• 0
0
votes
1
reply
1.1k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
biomyscience
• 0
0
votes
1
reply
876
views
Meta analysis
DEGseq
Metanalysis
updated 3.4 years ago by
Kevin Blighe
★ 4.0k • written 3.4 years ago by
biomyscience
• 0
1
vote
2
replies
1.1k
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 3.9 years ago by
swbarnes2
★ 1.4k • written 3.9 years ago by
Nicolò
• 0
1
vote
7
replies
1.8k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
4.1 years ago • updated 4.0 years ago
decppced
• 0
0
votes
3
replies
1.4k
views
DeSeq2- design experiment
rnaseq
degseq
7.5 years ago
laksharikrish
• 0
0
votes
1
reply
1.4k
views
Problem with DEGseq/samWrapper
degseq
updated 7.8 years ago by
ab.tsubaki
• 0 • written 10.3 years ago by
jovel_juan
▴ 30
0
votes
0
replies
1.1k
views
Regarding q-value
DEGseq
DEGseq
11.8 years ago
deepika lakhwani
▴ 170
0
votes
1
reply
1.6k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 12.2 years ago by
delhomme@embl.de
★ 1.2k • written 12.2 years ago by
Guest User
★ 13k
0
votes
3
replies
1.8k
views
Analysis of public GEO datasets - NGS
DEGseq
DEGseq
updated 12.5 years ago by
Aliaksei Holik
▴ 350 • written 12.5 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
12.5 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
4.4k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 12.6 years ago by
Gordon Smyth
52k • written 12.6 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.4k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.1 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.2 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.2 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.1k
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
14.7 years ago
sunghee OH
▴ 50
0
votes
1
reply
1.2k
views
A question on DESeq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 14.7 years ago by
Simon Anders
★ 3.8k • written 14.7 years ago by
sunghee OH
▴ 50
0
votes
8
replies
2.5k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 14.9 years ago by
Naomi Altman
★ 6.0k • written 14.9 years ago by
michael watson IAH-C
★ 3.4k
0
votes
3
replies
1.9k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 15.5 years ago by
Ulrike Goebel
▴ 110 • written 15.5 years ago by
Naomi Altman
★ 6.0k
0
votes
0
replies
1.2k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
15.5 years ago
Likun Wang
▴ 50
28 results • Page
1 of 1
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Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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