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LIMMA
•
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0
votes
2
replies
100
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
19 hours ago • updated 6 hours ago
SSSJec
• 0
0
votes
1
reply
119
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
taur.vil
• 0
13
votes
16
replies
1.0k
views
Why p value inconsistent when using different number of pathway score?
limma
updated 10 hours ago by
Gordon Smyth
50k • written 9 days ago by
Chris
• 0
0
votes
2
replies
181
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
10 days ago • updated 8 days ago
catv
• 0
3
votes
1
reply
150
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
Shaimaa Gamal
• 0
0
votes
7
replies
275
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
12 days ago • updated 7 days ago
hortense96
• 0
5
votes
9
replies
882
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
19 days ago • updated 11 days ago
Chris
• 0
1
vote
3
replies
333
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 15 days ago by
Gordon Smyth
50k • written 20 days ago by
Simran
• 0
2
votes
6
replies
368
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
21 days ago
Chris
• 0
0
votes
1
reply
152
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 24 days ago by
Gordon Smyth
50k • written 24 days ago by
avery
• 0
0
votes
4
replies
294
views
Help with design.matrix
limma
24 days ago • updated 23 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
420
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 25 days ago by
Gordon Smyth
50k • written 26 days ago by
jari.karppinen
• 0
0
votes
2
replies
178
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
27 days ago • updated 26 days ago
Gimena
• 0
15
votes
22
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 9 days ago
Chris
• 0
2
votes
8
replies
508
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
5
votes
25
replies
841
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 25 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
7
votes
6
replies
439
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
225
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
scoops_streams_06
• 0
0
votes
4
replies
380
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
442
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
2
votes
2
replies
251
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
6 weeks ago
Sabiha
▴ 20
0
votes
2
replies
254
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 weeks ago
kcarey
• 0
2
votes
6
replies
469
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
7 weeks ago • updated 5 weeks ago
Lily Cheang
▴ 10
3
votes
8
replies
491
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago
dl17032000
• 0
8
votes
6
replies
435
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
146
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
3
replies
274
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Laura
• 0
0
votes
4
replies
287
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
8 weeks ago
mperalc
• 0
2
votes
1
reply
250
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
610
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
292
views
Bioconductor unreachable?
limma
9 weeks ago
edoardo
• 0
0
votes
9
replies
541
views
limma fo continous variables
limma
DEGseq
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
mia
• 0
0
votes
2
replies
276
views
limma model matrix questions
limmaGUI
limma
pairedsamples
10 weeks ago
whyw6948
• 0
0
votes
2
replies
308
views
Limma with replicates at different time points
RNAs
limma
Differen
10 weeks ago • updated 9 weeks ago
alessandro
• 0
2
votes
1
reply
287
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 10 weeks ago by
ATpoint
★ 4.1k • written 10 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
337
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
355
views
limma with interaction term
R
biostatistics
limma
Epigenetics
11 weeks ago • updated 9 weeks ago
Jitendra
▴ 10
3
votes
2
replies
284
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
11 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
317
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago
COPD_Project
• 0
1
vote
4
replies
395
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Jitendra
▴ 10
2
votes
2
replies
274
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
11 weeks ago
SamGG
▴ 350
4
votes
3
replies
343
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
358
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
248
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
12 weeks ago
Lily Cheang
▴ 10
1
vote
3
replies
386
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 12 weeks ago by
pl23
• 0
1
vote
2
replies
329
views
Longitudinal analysis in Limma
limma
3 months ago • updated 12 weeks ago
COPD_Project
• 0
2
votes
2
replies
281
views
Using limma for controlling age variable
linearmodeling
limma
3 months ago
Matej
• 0
4
votes
6
replies
569
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 11 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
5
replies
532
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Xiao
• 0
2
votes
4
replies
502
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
michelafrancesconi8
• 0
50 results • Page
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Replies
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
alserg
▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Robert for an educative response!
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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