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25
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FilterByExpr low counts with small sample size
edgeR
3 hours ago • updated 1 hour ago
Jonathan
▴ 10
3
votes
3
replies
244
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 9 days ago by
Netanel
• 0
1
vote
3
replies
285
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 2 days ago by
Gordon Smyth
50k • written 7 days ago by
Simran
• 0
5
votes
6
replies
355
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 days ago by
ATpoint
★ 4.0k • written 8 days ago by
nhaus
▴ 30
1
vote
3
replies
210
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 11 days ago by
James W. MacDonald
65k • written 12 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
132
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
14 days ago
Marianna
▴ 20
0
votes
4
replies
376
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
16 days ago • updated 15 days ago
Lucy
▴ 60
3
votes
5
replies
322
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 17 days ago by
Gordon Smyth
50k • written 19 days ago by
Fabian
• 0
0
votes
6
replies
299
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 19 days ago by
Gordon Smyth
50k • written 20 days ago by
Faisal
• 0
0
votes
1
reply
199
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 27 days ago by
scoops_streams_06
• 0
5
votes
3
replies
660
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 20 days ago by
Gordon Smyth
50k • written 27 days ago by
Jack S.
▴ 50
2
votes
3
replies
262
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
JKim
• 0
0
votes
2
replies
243
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
z_bahari
• 0
2
votes
2
replies
233
views
between lane normalization upper quantile
EDASeq
edgeR
4 weeks ago
elesofi
• 0
2
votes
2
replies
233
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
4 weeks ago
Sabiha
▴ 20
0
votes
3
replies
350
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 10 weeks ago by
pl23
• 0
3
votes
4
replies
360
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
203
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Fabian
• 0
0
votes
11
replies
664
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
mico
• 0
0
votes
1
reply
226
views
ExactTest vs QLFTest
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
fr8712ca-s
• 0
1
vote
6
replies
428
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
7 weeks ago
mico
• 0
2
votes
6
replies
376
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
8 weeks ago
tsl0026
• 0
5
votes
4
replies
360
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
8 weeks ago • updated 7 weeks ago
pl23
• 0
0
votes
8
replies
586
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
9 weeks ago • updated 8 weeks ago
Marianna
▴ 20
3
votes
2
replies
358
views
How does one test for interactions in EdgeR?
edgeR
9 weeks ago
pl23
• 0
0
votes
4
replies
313
views
Nested paired design
edgeR
10 weeks ago • updated 9 weeks ago
manduchi
▴ 10
1
vote
2
replies
292
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
10 weeks ago • updated 9 weeks ago
mico
• 0
2
votes
3
replies
327
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Shaimaa Gamal
• 0
4
votes
4
replies
410
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 11 weeks ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
6
votes
7
replies
529
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
aa.machado001
• 0
1
vote
8
replies
508
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
sat
• 0
0
votes
0
replies
217
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
12 weeks ago
Jawahar
• 0
2
votes
4
replies
516
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
12 weeks ago
Sabiha
▴ 20
0
votes
3
replies
307
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
annasoudi
• 0
3
votes
3
replies
621
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 12 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
3 months ago
Luca
• 0
0
votes
1
reply
284
views
download problem
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
theokirkland3
• 0
0
votes
5
replies
583
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
3 months ago • updated 11 weeks ago
Lucy
▴ 60
1
vote
2
replies
415
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
5
votes
2
replies
503
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
1
vote
2
replies
369
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Jurgen
• 0
7
votes
2
replies
708
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
0
votes
3
replies
427
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago
Karthik
• 0
4
votes
2
replies
567
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
6
votes
7
replies
898
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 5 months ago by
ATpoint
★ 4.0k • written 6 months ago by
jonas.freimuth
▴ 20
0
votes
0
replies
255
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
1
vote
3
replies
429
views
edgeR: Time course RNA-seq experiments
edgeR
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
SuperDad
• 0
0
votes
1
reply
422
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Giuseppe
• 0
1
vote
6
replies
2.6k
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 7.4 years ago by
Camila Orellana
▴ 10
1
vote
4
replies
696
views
MDS plot edgeR
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
50 results • Page
1 of 1
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Replies
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Answer: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
You don't explain how many samples you have (columns of data), but the warning message shown in your post would arise if there are in fact …
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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