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limma
•
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0
votes
0
replies
12
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
1 hour ago
catv
• 0
0
votes
1
reply
59
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
0
votes
6
replies
153
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
hortense96
• 0
5
votes
9
replies
797
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
Chris
• 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
2
votes
6
replies
309
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
139
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 13 days ago by
avery
• 0
0
votes
4
replies
281
views
Help with design.matrix
limma
13 days ago • updated 12 days ago
andrea.rodriguez-martinez13
• 0
1
vote
4
replies
398
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 16 days ago by
jari.karppinen
• 0
0
votes
2
replies
162
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago • updated 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
473
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
Amit
• 0
5
votes
25
replies
783
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
410
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
205
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
360
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
4 weeks ago • updated 24 days ago
Efra
• 0
5
votes
7
replies
414
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
238
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
226
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago
kcarey
• 0
2
votes
6
replies
435
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
476
views
Constrast for Time Course Experiments using Limma
limma
6 weeks ago
dl17032000
• 0
8
votes
6
replies
418
views
DGE analysis with LIMMA
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Amit
• 0
0
votes
0
replies
137
views
Can I combine collinear variables into a single value
BatchEffect
limma
7 weeks ago
Harrsha
• 0
0
votes
3
replies
264
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
262
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
237
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
585
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
266
views
Bioconductor unreachable?
limma
8 weeks ago
edoardo
• 0
0
votes
9
replies
507
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
264
views
limma model matrix questions
limmaGUI
limma
pairedsamples
8 weeks ago
whyw6948
• 0
0
votes
2
replies
292
views
Limma with replicates at different time points
RNAs
limma
Differen
9 weeks ago • updated 7 weeks ago
alessandro
• 0
2
votes
1
reply
275
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
326
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
325
views
limma with interaction term
R
biostatistics
limma
Epigenetics
10 weeks ago • updated 7 weeks ago
Jitendra
▴ 10
3
votes
2
replies
259
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
10 weeks ago
Shaimaa Gamal
• 0
2
votes
3
replies
290
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
350
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
262
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
10 weeks ago
SamGG
▴ 350
4
votes
3
replies
315
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
333
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
236
views
Pairwise analysis of DESeq result and limma result
DESeq2
limma
10 weeks ago
Lily Cheang
▴ 10
0
votes
3
replies
352
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
308
views
Longitudinal analysis in Limma
limma
11 weeks ago
COPD_Project
• 0
2
votes
2
replies
259
views
Using limma for controlling age variable
linearmodeling
limma
11 weeks ago
Matej
• 0
4
votes
6
replies
539
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
493
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
474
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
280
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
390
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
595
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
50 results • Page
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Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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