Showing : limma • reset
1
vote
2
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249
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
263
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
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
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA limma
16 days ago Chris ▴ 10
0
votes
3
replies
270
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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
189
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
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
5
votes
3
replies
304
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Log-cpm values from limma
limma edgeR RNASeq
updated 7 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
5
votes
9
replies
973
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 28 days ago Chris ▴ 10
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
1
reply
185
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
207
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
559
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
250
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
481
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
replies
288
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
2
votes
6
replies
549
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
164
views
Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
votes
3
replies
317
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
4
replies
322
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 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
3
votes
5
replies
664
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
1
vote
2
replies
337
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
votes
9
replies
588
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
2
replies
315
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
0
votes
2
replies
345
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
382
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
392
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
346
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
1
vote
4
replies
437
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
2
votes
2
replies
303
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
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
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
0
votes
2
replies
292
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
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…
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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