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limma
•
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1
vote
2
replies
152
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
1 day ago • updated 15 hours ago
Dylan.Sheerin
• 0
1
vote
1
reply
118
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
zzrammal
• 0
3
votes
10
replies
259
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 3 hours ago by
James W. MacDonald
65k • written 3 days ago by
Abbey
• 0
1
vote
2
replies
357
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
Kim
• 0
0
votes
1
reply
124
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
c53aba27
• 0
3
votes
4
replies
236
views
Help with error using camera() in limma
CAMERA
limma
10 days ago • updated 9 days ago
Chris
• 0
0
votes
3
replies
255
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 10 days ago by
James W. MacDonald
65k • written 11 days ago by
SSSJec
• 0
0
votes
2
replies
174
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 17 days ago by
taur.vil
• 0
0
votes
2
replies
221
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
21 days ago • updated 18 days ago
catv
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
20 days ago • updated 8 days ago
Chris
• 0
5
votes
3
replies
258
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 hours ago by
Gordon Smyth
50k • written 22 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
327
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
23 days ago • updated 17 days ago
hortense96
• 0
1
vote
3
replies
356
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 25 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
5
votes
9
replies
940
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 22 days ago
Chris
• 0
2
votes
6
replies
430
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
4 weeks ago
Chris
• 0
0
votes
1
reply
175
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
avery
• 0
0
votes
4
replies
321
views
Help with design.matrix
limma
5 weeks ago • updated 4 weeks ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
449
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
jari.karppinen
• 0
0
votes
2
replies
198
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
5 weeks ago
Gimena
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 10 days ago
Chris
• 0
2
votes
8
replies
550
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
5
votes
25
replies
958
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Jitendra
▴ 10
7
votes
6
replies
469
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
0
votes
1
reply
238
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
scoops_streams_06
• 0
0
votes
4
replies
401
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
7 weeks ago • updated 6 weeks ago
Efra
• 0
5
votes
7
replies
468
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
2
votes
2
replies
270
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
8 weeks ago
Sabiha
▴ 20
0
votes
2
replies
290
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
8 weeks ago
kcarey
• 0
1
vote
3
replies
421
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
2
votes
6
replies
506
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
9 weeks ago • updated 6 weeks ago
Lily Cheang
▴ 10
3
votes
8
replies
528
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago
dl17032000
• 0
8
votes
6
replies
480
views
DGE analysis with LIMMA
limma
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Amit
• 0
0
votes
0
replies
156
views
Can I combine collinear variables into a single value
BatchEffect
limma
10 weeks ago
Harrsha
• 0
0
votes
3
replies
308
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Laura
• 0
0
votes
4
replies
309
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
10 weeks ago
mperalc
• 0
3
votes
5
replies
641
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 9 weeks ago by
Michael Love
42k • written 10 weeks ago by
sap275
▴ 10
2
votes
1
reply
270
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 10 weeks ago by
sap275
▴ 10
1
vote
2
replies
318
views
Bioconductor unreachable?
limma
11 weeks ago
edoardo
• 0
0
votes
9
replies
568
views
limma fo continous variables
limma
DEGseq
updated 10 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
mia
• 0
0
votes
2
replies
301
views
limma model matrix questions
limmaGUI
limma
pairedsamples
11 weeks ago
whyw6948
• 0
0
votes
2
replies
330
views
Limma with replicates at different time points
RNAs
limma
Differen
12 weeks ago • updated 10 weeks ago
alessandro
• 0
2
votes
1
reply
311
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 12 weeks ago by
ATpoint
★ 4.1k • written 12 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
365
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
380
views
limma with interaction term
R
biostatistics
limma
Epigenetics
3 months ago • updated 10 weeks ago
Jitendra
▴ 10
3
votes
2
replies
304
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
3 months ago
Shaimaa Gamal
• 0
2
votes
3
replies
334
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago
COPD_Project
• 0
2
votes
2
replies
294
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
3 months ago
SamGG
▴ 350
1
vote
4
replies
421
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 12 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Jitendra
▴ 10
4
votes
3
replies
367
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
378
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
50 results • Page
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Replies
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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