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Limma
•
reset
0
votes
0
replies
35
views
Log-cpm values from limma
limma
edgeR
RNASeq
19 hours ago
Shaimaa Gamal
• 0
0
votes
6
replies
147
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
hortense96
• 0
5
votes
9
replies
785
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 13 hours ago
Chris
• 0
1
vote
3
replies
298
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 3 days ago by
Gordon Smyth
50k • written 8 days ago by
Simran
• 0
2
votes
6
replies
305
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
10 days ago
Chris
• 0
0
votes
1
reply
138
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
avery
• 0
0
votes
4
replies
279
views
Help with design.matrix
limma
13 days ago • updated 12 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
397
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 14 days ago by
Gordon Smyth
50k • written 15 days ago by
jari.karppinen
• 0
0
votes
2
replies
161
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
15 days ago
Gimena
• 0
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 11 days ago
Chris
• 0
2
votes
8
replies
472
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 21 days ago by
Gordon Smyth
50k • written 23 days ago by
Amit
• 0
5
votes
25
replies
777
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 24 days ago by
Jitendra
▴ 10
7
votes
6
replies
409
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 27 days ago by
Gordon Smyth
50k • written 27 days ago by
Amit
• 0
0
votes
1
reply
203
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
scoops_streams_06
• 0
0
votes
4
replies
358
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
4 weeks ago • updated 23 days ago
Efra
• 0
5
votes
7
replies
411
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 22 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
2
votes
2
replies
236
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 weeks ago
Sabiha
▴ 20
0
votes
2
replies
225
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago
kcarey
• 0
2
votes
6
replies
432
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
6 weeks ago • updated 24 days ago
Lily Cheang
▴ 10
3
votes
8
replies
473
views
Constrast for Time Course Experiments using Limma
limma
6 weeks ago
dl17032000
• 0
8
votes
6
replies
415
views
DGE analysis with LIMMA
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
0
votes
0
replies
135
views
Can I combine collinear variables into a single value
BatchEffect
limma
6 weeks ago
Harrsha
• 0
0
votes
3
replies
263
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Laura
• 0
0
votes
4
replies
261
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
7 weeks ago
mperalc
• 0
2
votes
1
reply
236
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 7 weeks ago by
Michael Love
41k • written 7 weeks ago by
sap275
▴ 10
3
votes
5
replies
584
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 6 weeks ago by
Michael Love
41k • written 7 weeks ago by
sap275
▴ 10
1
vote
2
replies
264
views
Bioconductor unreachable?
limma
8 weeks ago
edoardo
• 0
0
votes
9
replies
502
views
limma fo continous variables
limma
DEGseq
updated 7 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
mia
• 0
0
votes
2
replies
263
views
limma model matrix questions
limmaGUI
limma
pairedsamples
8 weeks ago
whyw6948
• 0
0
votes
2
replies
291
views
Limma with replicates at different time points
RNAs
limma
Differen
8 weeks ago • updated 7 weeks ago
alessandro
• 0
2
votes
1
reply
273
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 9 weeks ago by
ATpoint
★ 4.0k • written 9 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
325
views
CAMERA + Gene Ontology Gene Sets
GO
limma
CAMERA
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Tyler Sagendorf
▴ 10
0
votes
4
replies
323
views
limma with interaction term
R
biostatistics
limma
Epigenetics
9 weeks ago • updated 7 weeks ago
Jitendra
▴ 10
3
votes
2
replies
258
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
10 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
287
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
10 weeks ago • updated 9 weeks ago
COPD_Project
• 0
1
vote
4
replies
349
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jitendra
▴ 10
2
votes
2
replies
261
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
10 weeks ago
SamGG
▴ 350
4
votes
3
replies
313
views
voom with quality weights after RUV correction
RUVSeq
limma
DifferentialExpression
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Shaimaa Gamal
• 0
2
votes
3
replies
332
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
0
votes
2
replies
234
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
10 weeks ago
Lily Cheang
▴ 10
0
votes
3
replies
351
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
1
vote
2
replies
306
views
Longitudinal analysis in Limma
limma
11 weeks ago
COPD_Project
• 0
2
votes
2
replies
258
views
Using limma for controlling age variable
linearmodeling
limma
11 weeks ago
Matej
• 0
4
votes
6
replies
538
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 10 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
5
replies
492
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Xiao
• 0
2
votes
4
replies
473
views
Different genes expression with limma
DESeq2
DifferentialExpression
limma
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
michelafrancesconi8
• 0
2
votes
1
reply
278
views
removeBatchEffect with non-linear model fit
limma
DESeq2
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
georgii.vdovin
• 0
0
votes
3
replies
389
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip
limma
goana
updated 4 months ago by
SamGG
▴ 350 • written 4 months ago by
samagbeyimodupe
• 0
2
votes
4
replies
593
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
kyj2226
• 0
1
vote
2
replies
447
views
Assess fit of variance prior
limma
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Frederik Ziebell
▴ 20
50 results • Page
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
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• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
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• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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