Showing : limma • reset
2
votes
2
replies
262
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
9 days ago • updated 3 days ago zzrammal • 0
3
votes
10
replies
433
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 6 days ago by 65k • written 9 days ago by • 0
5
votes
3
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304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 days ago by 50k • written 28 days ago by • 0
1
vote
2
replies
247
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
8 days ago • updated 7 days ago Dylan.Sheerin • 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 8 days ago by 50k • written 5.6 years ago by ▴ 10
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 days ago by 50k • written 13 days ago by • 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
2
replies
187
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 24 days ago by • 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
26 days ago • updated 15 days ago Chris ▴ 10
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA limma
16 days ago Chris ▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 16 days ago by • 0 • written 8.0 years ago by • 0
0
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3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 16 days ago by • 0 • written 13.1 years ago by ▴ 10
0
votes
3
replies
270
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 16 days ago by 65k • written 17 days ago by • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 16 days ago Chris ▴ 10
0
votes
7
replies
352
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
29 days ago • updated 23 days ago hortense96 • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 23 days ago by • 0 • written 7.8 years ago by ▴ 30
0
votes
2
replies
235
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
27 days ago • updated 24 days ago catv • 0
5
votes
9
replies
968
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 28 days ago Chris ▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 29 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
628
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
6
replies
451
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
votes
4
replies
328
views
Help with design.matrix
limma
5 weeks ago andrea.rodriguez-martinez13 • 0
0
votes
1
reply
184
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
1
vote
4
replies
460
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
votes
25
replies
985
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
0
votes
2
replies
205
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
2
votes
8
replies
558
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
7
replies
480
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
4
replies
408
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
8 weeks ago • updated 7 weeks ago Efra • 0
2
votes
6
replies
547
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 10
7
votes
6
replies
478
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
249
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
2
replies
310
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
2
votes
2
replies
287
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
vote
3
replies
436
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
8
replies
539
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
0
votes
3
replies
316
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
3
votes
5
replies
663
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
8
votes
6
replies
500
views
DGE analysis with LIMMA
limma
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
votes
0
replies
163
views
Can I combine collinear variables into a single value
BatchEffect limma
10 weeks ago Harrsha • 0
0
votes
4
replies
321
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
votes
2
replies
344
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 11 weeks ago alessandro • 0
0
votes
9
replies
587
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
1
reply
276
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
0
votes
4
replies
389
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
1
vote
2
replies
336
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
votes
2
replies
313
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
2
votes
1
reply
318
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
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So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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