Showing : limma • reset
0
votes
1
reply
22
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 1 hour ago by 65k • written 2 hours ago by • 0
0
votes
1
reply
30
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 2 hours ago by 65k • written 4 hours ago by • 0
1
vote
2
replies
336
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 3 days ago by 50k • written 3 days ago by • 0
0
votes
1
reply
108
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 4 days ago by 50k • written 5 days ago by • 0
3
votes
4
replies
218
views
Help with error using camera() in limma
CAMERA limma
7 days ago • updated 6 days ago Chris • 0
0
votes
3
replies
246
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 7 days ago by 65k • written 8 days ago by • 0
0
votes
2
replies
170
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 14 days ago by • 0
0
votes
2
replies
213
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
18 days ago • updated 15 days ago catv • 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 6 days ago Chris • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
0
votes
7
replies
323
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
20 days ago • updated 14 days ago hortense96 • 0
1
vote
3
replies
352
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 22 days ago by 50k • written 27 days ago by • 0
5
votes
9
replies
932
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
26 days ago • updated 19 days ago Chris • 0
2
votes
6
replies
405
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
29 days ago • updated 28 days ago Chris • 0
0
votes
1
reply
171
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
4
replies
315
views
Help with design.matrix
limma
4 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
444
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
2
replies
195
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago Gimena • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 7 days ago Chris • 0
2
votes
8
replies
544
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
5
votes
25
replies
939
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 4 weeks ago by 50k • written 6 weeks ago by ▴ 10
7
votes
6
replies
459
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
1
reply
236
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
399
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
7 weeks ago • updated 6 weeks ago Efra • 0
5
votes
7
replies
463
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
2
replies
266
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
votes
2
replies
273
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
vote
3
replies
412
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
votes
6
replies
492
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 6 weeks ago Lily Cheang ▴ 10
3
votes
8
replies
519
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago • updated 8 weeks ago dl17032000 • 0
8
votes
6
replies
464
views
DGE analysis with LIMMA
limma
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
0
replies
153
views
Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
votes
3
replies
294
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
4
replies
304
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago • updated 9 weeks ago mperalc • 0
3
votes
5
replies
634
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
2
votes
1
reply
267
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
1
vote
2
replies
312
views
Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
votes
9
replies
564
views
limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
2
replies
297
views
limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
0
votes
2
replies
323
views
Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 10 weeks ago alessandro • 0
2
votes
1
reply
305
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
vote
3
replies
359
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
0
votes
4
replies
375
views
limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 10 weeks ago Jitendra ▴ 10
3
votes
2
replies
298
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
2
votes
3
replies
331
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago COPD_Project • 0
2
votes
2
replies
292
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
1
vote
4
replies
415
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 3 months ago by ▴ 10
4
votes
3
replies
360
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
372
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Popular Question to priyanka.m • 0
Locations • All
United States, 1 minute ago
Switzerland, 5 minutes ago
India, 10 minutes ago
United States, 27 minutes ago
United States, 28 minutes ago
Traffic: 738 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