Showing : Limma • reset
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 4 hours ago Chris • 0
3
votes
4
replies
112
views
Help with error using camera() in limma
CAMERA limma
16 hours ago • updated 11 hours ago Chris • 0
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 13 hours ago by • 0 • written 7.9 years ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 13 hours ago by • 0 • written 13.0 years ago by ▴ 10
0
votes
3
replies
174
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 15 hours ago by 65k • written 1 day ago by • 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 15 hours ago Chris • 0
0
votes
7
replies
284
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 • 0 • written 7.7 years ago by ▴ 30
0
votes
1
reply
126
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 8 days ago by 50k • written 8 days ago by • 0
0
votes
2
replies
185
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 days ago • updated 8 days ago catv • 0
3
votes
1
reply
152
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 12 days ago by • 0
5
votes
9
replies
891
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
20 days ago • updated 12 days ago Chris • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 13 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
588
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 14 days ago by 41k • written 6 months ago by • 0
1
vote
3
replies
337
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 15 days ago by 50k • written 21 days ago by • 0
2
votes
6
replies
376
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
22 days ago Chris • 0
0
votes
4
replies
298
views
Help with design.matrix
limma
25 days ago • updated 24 days ago andrea.rodriguez-martinez13 • 0
0
votes
1
reply
154
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 24 days ago by 50k • written 25 days ago by • 0
1
vote
4
replies
423
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 26 days ago by 50k • written 27 days ago by • 0
5
votes
25
replies
845
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 26 days ago by 50k • written 5 weeks ago by ▴ 10
0
votes
2
replies
180
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
27 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 50k • written 9.8 years ago by ▴ 40
2
votes
8
replies
511
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
7
replies
443
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
382
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
471
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
440
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
226
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
2
replies
256
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
2
votes
2
replies
252
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
392
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
3
votes
8
replies
493
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago • updated 7 weeks ago dl17032000 • 0
0
votes
3
replies
275
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
3
votes
5
replies
612
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
8
votes
6
replies
439
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
0
replies
147
views
Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
votes
4
replies
288
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago • updated 8 weeks ago mperalc • 0
0
votes
2
replies
309
views
Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 9 weeks ago alessandro • 0
0
votes
9
replies
545
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
1
reply
253
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
votes
4
replies
359
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
1
vote
2
replies
297
views
Bioconductor unreachable?
limma
9 weeks ago edoardo • 0
0
votes
2
replies
277
views
limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
2
votes
1
reply
288
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
1
vote
3
replies
340
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 10
1
vote
4
replies
396
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
2
votes
3
replies
319
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago COPD_Project • 0
3
votes
2
replies
287
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
4
votes
6
replies
573
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
2
votes
2
replies
277
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
50 results • Page 1 of 1
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Awards • All
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Locations • All
The city by the bay, 1 hour ago
Canada, 1 hour ago
USA, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
Canada, 2 hours ago
Traffic: 386 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6