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LIMMA
•
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14
votes
17
replies
1.0k
views
Why p value inconsistent when using different number of pathway score?
limma
9 days ago • updated just now
Chris
• 0
0
votes
2
replies
122
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
23 hours ago • updated 10 hours ago
SSSJec
• 0
0
votes
7
replies
277
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
13 days ago • updated 7 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 7 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
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
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
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
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
5
votes
9
replies
885
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
19 days ago • updated 12 days ago
Chris
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 12 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
584
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 13 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
3
replies
334
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
371
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
4
replies
296
views
Help with design.matrix
limma
24 days ago • updated 23 days ago
andrea.rodriguez-martinez13
• 0
0
votes
1
reply
153
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
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 27 days ago by
jari.karppinen
• 0
5
votes
25
replies
843
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
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
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
2
votes
8
replies
509
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
7
replies
442
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 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
2
votes
6
replies
470
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
7 weeks ago • updated 5 weeks ago
Lily Cheang
▴ 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
2
replies
254
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 weeks ago
kcarey
• 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
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
3
votes
8
replies
491
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago
dl17032000
• 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
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
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
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
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
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
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
0
votes
4
replies
357
views
limma with interaction term
R
biostatistics
limma
Epigenetics
11 weeks ago • updated 9 weeks ago
Jitendra
▴ 10
1
vote
2
replies
293
views
Bioconductor unreachable?
limma
9 weeks ago
edoardo
• 0
0
votes
2
replies
276
views
limma model matrix questions
limmaGUI
limma
pairedsamples
10 weeks ago
whyw6948
• 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
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
3
replies
317
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago
COPD_Project
• 0
3
votes
2
replies
284
views
Design matrix after RUVg correction
RUVSeq
limma
DifferentialExpression
11 weeks ago
Shaimaa Gamal
• 0
4
votes
6
replies
570
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
2
votes
2
replies
275
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
12 weeks ago • updated 11 weeks ago
SamGG
▴ 350
4
votes
3
replies
343
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
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
Sorry, for questions about statistical analysis plan and interpretation of results, I recommend to work with a local statistician or someon…
Answer: Fold change calculation in Diffbind vs. DESEQ2?
by
Michael Love
41k
There was a recent DiffBind question on the support site that noticed the same thing, try searching recent DiffBind posts.
Answer: Timecourse RNASeq analysis
by
Michael Love
41k
There are many choices for time course, and we have an example in our workflow (rnaseqGene). Otherwise, I recommend to consult a local …
Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar
by
Michael Love
41k
You can either turn off independent filtering in `results` or use `ihw` see the vignette.
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Gordon for a detail guide! You have a great memory of time. GSVA also do differential express at pathway level (https://bioconductor…
Votes
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
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
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