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limma
•
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0
votes
0
replies
16
views
Gene-by-sample covariates in limma
Metabolomics
limma
3 hours ago
c53aba27
• 0
3
votes
4
replies
166
views
Help with error using camera() in limma
CAMERA
limma
2 days ago
Chris
• 0
0
votes
3
replies
207
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
0
votes
2
replies
150
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
0
votes
2
replies
195
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
13 days ago • updated 10 days ago
catv
• 0
3
votes
1
reply
160
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
289
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
5
votes
9
replies
898
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago
Chris
• 0
1
vote
3
replies
342
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
2
votes
6
replies
387
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
24 days ago
Chris
• 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 26 days ago by
avery
• 0
0
votes
4
replies
302
views
Help with design.matrix
limma
27 days ago • updated 26 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
428
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
jari.karppinen
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago
Gimena
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
2
votes
8
replies
518
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
5
votes
25
replies
874
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
7
votes
6
replies
447
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
1
reply
231
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
scoops_streams_06
• 0
0
votes
4
replies
386
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
6 weeks ago • updated 5 weeks ago
Efra
• 0
5
votes
7
replies
448
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
2
votes
2
replies
257
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
7 weeks ago
Sabiha
▴ 20
0
votes
2
replies
259
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
7 weeks ago
kcarey
• 0
2
votes
6
replies
480
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
8 weeks ago • updated 5 weeks ago
Lily Cheang
▴ 10
3
votes
8
replies
496
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago
dl17032000
• 0
8
votes
6
replies
448
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Amit
• 0
0
votes
0
replies
148
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
3
replies
280
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Laura
• 0
0
votes
4
replies
296
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
9 weeks ago
mperalc
• 0
2
votes
1
reply
259
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 9 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
3
votes
5
replies
615
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 9 weeks ago by
sap275
▴ 10
1
vote
2
replies
300
views
Bioconductor unreachable?
limma
10 weeks ago
edoardo
• 0
0
votes
9
replies
552
views
limma fo continous variables
limma
DEGseq
updated 9 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
mia
• 0
0
votes
2
replies
285
views
limma model matrix questions
limmaGUI
limma
pairedsamples
10 weeks ago
whyw6948
• 0
0
votes
2
replies
313
views
Limma with replicates at different time points
RNAs
limma
Differen
10 weeks ago • updated 9 weeks ago
alessandro
• 0
2
votes
1
reply
290
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
345
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
364
views
limma with interaction term
R
biostatistics
limma
Epigenetics
11 weeks ago • updated 9 weeks ago
Jitendra
▴ 10
3
votes
2
replies
290
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
12 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
324
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago • updated 11 weeks ago
COPD_Project
• 0
1
vote
4
replies
404
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Jitendra
▴ 10
2
votes
2
replies
284
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
12 weeks ago
SamGG
▴ 350
4
votes
3
replies
348
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
364
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 12 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
252
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
12 weeks ago
Lily Cheang
▴ 10
1
vote
3
replies
396
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
1
vote
2
replies
336
views
Longitudinal analysis in Limma
limma
3 months ago
COPD_Project
• 0
2
votes
2
replies
292
views
Using limma for controlling age variable
linearmodeling
limma
3 months ago
Matej
• 0
4
votes
6
replies
585
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 12 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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