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EdgeR
•
reset
1
vote
2
replies
1.3k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
24 months ago • updated 23 months ago
Sabiha
▴ 20
5
votes
2
replies
1.6k
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
annikagable
• 0
1
vote
2
replies
1.4k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
Jurgen
• 0
12
votes
5
replies
5.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 6 months ago by
Geoff
• 0 • written 2.0 years ago by
annikagable
• 0
0
votes
3
replies
1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
2.0 years ago
Karthik
• 0
5
votes
2
replies
2.2k
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
alvaroperona1
▴ 10
6
votes
7
replies
1.8k
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
jonas.freimuth
▴ 20
0
votes
0
replies
737
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.1 years ago
Florian
• 0
1
vote
3
replies
909
views
edgeR: Time course RNA-seq experiments
edgeR
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
SuperDad
• 0
0
votes
1
reply
863
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Giuseppe
• 0
1
vote
6
replies
3.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 9.1 years ago by
Camila Orellana
▴ 10
1
vote
4
replies
1.3k
views
MDS plot edgeR
edgeR
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
jbono
▴ 10
3
votes
3
replies
1.0k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
stuartthafass
• 0
1
vote
2
replies
2.0k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
2.2 years ago
petertam1343
• 0
1
vote
5
replies
1.3k
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
Mohamed
▴ 30
3
votes
3
replies
1.1k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
2.2 years ago
Nisha
• 0
2
votes
3
replies
1.6k
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 2.3 years ago by
Vitor
• 0
1
vote
5
replies
1.3k
views
edgeR design/contrast matrix troubles
edgeR
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
alex.hart
• 0
0
votes
1
reply
858
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Sep
• 0
2
votes
4
replies
2.1k
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
hanc
▴ 10
0
votes
0
replies
2.1k
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
2.3 years ago
Gordon Smyth
53k
2
votes
7
replies
5.3k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 2.3 years ago by
lucap
• 0 • written 4.6 years ago by
Marianna
▴ 20
0
votes
8
replies
3.5k
views
Question about filterByExpr function edgeR
edgeR
2.3 years ago
lucap
• 0
0
votes
2
replies
777
views
EdgeR FTest
edgeR
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
nawaz.u.toyama
• 0
2
votes
5
replies
1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
2.3 years ago
duez.tolga
• 0
0
votes
2
replies
1.3k
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure
edgeR
2.3 years ago
greta
• 0
1
vote
1
reply
674
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
S
• 0
0
votes
9
replies
1.5k
views
estimateDisp() error
edgeR
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
ASNbioinf
• 0
4
votes
3
replies
1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
garcia
• 0
4
votes
9
replies
3.7k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
2.4 years ago
Luca
• 0
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
2.4 years ago
mohammedtoufiq91
▴ 10
6
votes
2
replies
1.3k
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
2.4 years ago
Josué
▴ 20
1
vote
1
reply
969
views
NA p values in edgeR results
DifferentialExpression
edgeR
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
miona.rankovic
• 0
1
vote
2
replies
1.1k
views
edgeR, RRBS Library size preparation
RRBSdata
edgeR
methylationArrayAnalysis
2.4 years ago
Krzysztof
• 0
1
vote
1
reply
823
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
Sara
• 0
3
votes
2
replies
1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
CDSPARKS
▴ 30
0
votes
5
replies
1.4k
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Cristina
• 0
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
mohammedtoufiq91
▴ 10
2
votes
1
reply
892
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
calvincornell1996
• 0
5
votes
11
replies
7.5k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 2.5 years ago by
Sabiha
▴ 20
5
votes
7
replies
2.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
980
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
simon
• 0
0
votes
1
reply
882
views
CI for logCPM (fitted values)
RNAseq
edgeR
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Lina
▴ 10
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma
RNASeq
edgeR
2.6 years ago
KATHERINE CHUERE NUNES
• 0
1
vote
2
replies
1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2
edgeR
RNASeq
DifferentialExpression
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Sofía
• 0
1
vote
3
replies
1.6k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower
edgeR
DifferentialExpression
limma
RNASeq
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Sara
• 0
0
votes
1
reply
1.1k
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
qiz218591
• 0
2
votes
1
reply
1.0k
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting
contrastCoding
edger
ExperimentalDesign
expressionDifferences
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
Hannes
• 0
0
votes
3
replies
1.3k
views
edgeR DEGs multilevel
edgeR
RNASeq
DifferentialRegulation
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
bioinfoWanderer
• 0
1
vote
1
reply
729
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2
edgeR
RNAseq
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
cmareevicars
• 0
2,031 results • Page
3 of 41
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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