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degseq
•
reset
0
votes
3
replies
552
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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 11 months ago by
Jonathan
• 0
0
votes
9
replies
2.2k
views
limma fo continous variables
limma
DEGseq
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
mia
• 0
0
votes
1
reply
977
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
sybyun419
• 0
0
votes
2
replies
1.0k
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
Shaimaa Gamal
• 0
2
votes
5
replies
1.8k
views
Create the design matrix
DEGseq
edgeR
RNASeq
2.8 years ago
Mohammad
• 0
0
votes
0
replies
1.4k
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
3.0 years ago
Rob
• 0
0
votes
2
replies
1.2k
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
CP
• 0
0
votes
2
replies
1.4k
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 3.3 years ago by
swbarnes2
★ 1.4k • written 3.3 years ago by
ac.mainul.mmb
• 0
1
vote
4
replies
1.5k
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 3.4 years ago by
Kevin Blighe
★ 4.0k • written 3.4 years ago by
beslinail
• 0
0
votes
1
reply
1.3k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 3.9 years ago by
James W. MacDonald
68k • written 3.9 years ago by
biomyscience
• 0
0
votes
1
reply
959
views
Meta analysis
DEGseq
Metanalysis
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
biomyscience
• 0
1
vote
2
replies
1.2k
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 4.5 years ago by
swbarnes2
★ 1.4k • written 4.5 years ago by
Nicolò
• 0
1
vote
7
replies
2.0k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
4.6 years ago
decppced
• 0
0
votes
3
replies
1.6k
views
DeSeq2- design experiment
rnaseq
degseq
8.0 years ago
laksharikrish
• 0
0
votes
1
reply
1.5k
views
Problem with DEGseq/samWrapper
degseq
updated 8.4 years ago by
ab.tsubaki
• 0 • written 10.9 years ago by
jovel_juan
▴ 30
0
votes
0
replies
1.2k
views
Regarding q-value
DEGseq
DEGseq
12.4 years ago
deepika lakhwani
▴ 170
0
votes
1
reply
1.7k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 12.8 years ago by
delhomme@embl.de
★ 1.2k • written 12.8 years ago by
Guest User
★ 13k
0
votes
3
replies
1.9k
views
Analysis of public GEO datasets - NGS
DEGseq
DEGseq
updated 13.1 years ago by
Aliaksei Holik
▴ 350 • written 13.1 years ago by
Guest User
★ 13k
0
votes
0
replies
1.5k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
13.1 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
4.5k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 13.2 years ago by
Gordon Smyth
53k • written 13.2 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.5k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.7 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.7 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.4k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.7 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
15.3 years ago
sunghee OH
▴ 50
0
votes
1
reply
1.3k
views
A question on DESeq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 15.3 years ago by
Simon Anders
★ 3.8k • written 15.3 years ago by
sunghee OH
▴ 50
0
votes
8
replies
2.9k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 15.4 years ago by
Naomi Altman
★ 6.0k • written 15.4 years ago by
michael watson IAH-C
★ 3.4k
0
votes
3
replies
2.1k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 16.0 years ago by
Ulrike Goebel
▴ 110 • written 16.1 years ago by
Naomi Altman
★ 6.0k
0
votes
0
replies
1.3k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
16.1 years ago
Likun Wang
▴ 50
28 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions
by
Michael Love
43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed
by
shepherl
4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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