Showing : limma • reset
1
vote
2
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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
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
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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
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
3
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4
replies
259
views
Help with error using camera() in limma
CAMERA limma
16 days ago Chris ▴ 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
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
0
votes
2
replies
236
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
27 days ago • updated 24 days ago catv • 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
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 days ago by 50k • written 28 days ago by • 0
0
votes
7
replies
352
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
29 days ago • updated 23 days ago hortense96 • 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
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
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
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
0
votes
4
replies
329
views
Help with design.matrix
limma
5 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
461
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
0
votes
2
replies
205
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 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
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
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
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 8 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
5
votes
7
replies
480
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 8 weeks ago by • 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
0
votes
2
replies
311
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
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
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
3
votes
8
replies
539
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
8
votes
6
replies
501
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
3
replies
316
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 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
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
2
votes
1
reply
276
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
1
vote
2
replies
336
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 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
0
votes
2
replies
314
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 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
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
1
vote
3
replies
381
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months 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
3
votes
2
replies
315
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
votes
3
replies
345
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
2
votes
2
replies
302
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
1
vote
4
replies
435
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
4
votes
3
replies
375
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
384
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • 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…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
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!!
Votes
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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