Showing : limma • reset
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 3 days ago by 50k • written 3 days ago by • 0
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2
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155
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 days ago • updated 3 days ago catv • 0
12
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12
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781
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Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by ★ 3.3k • written 5 days ago by • 0
3
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1
reply
120
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Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
0
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7
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252
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
8 days ago • updated 3 days ago hortense96 • 0
1
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3
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324
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 10 days ago by 50k • written 16 days ago by • 0
5
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9
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859
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Light difference when using coef vs omit a group when compare 3 groups.
limma
15 days ago • updated 7 days ago Chris • 0
2
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6
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351
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
17 days ago Chris • 0
0
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1
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147
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 20 days ago by 50k • written 20 days ago by • 0
0
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4
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291
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Help with design.matrix
limma
20 days ago • updated 19 days ago andrea.rodriguez-martinez13 • 0
1
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4
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415
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 21 days ago by 50k • written 22 days ago by • 0
0
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2
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174
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
23 days ago • updated 22 days ago Gimena • 0
15
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22
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1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
27 days ago • updated 5 days ago Chris • 0
2
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8
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497
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 29 days ago by 50k • written 4 weeks ago by • 0
5
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25
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825
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 21 days ago by 50k • written 4 weeks ago by ▴ 10
7
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6
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434
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Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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1
reply
218
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
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4
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373
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 4 weeks ago Efra • 0
5
votes
7
replies
430
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 29 days ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
247
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
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2
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243
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
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3
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370
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
2
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6
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451
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
3
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8
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482
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Constrast for Time Course Experiments using Limma
limma
7 weeks ago dl17032000 • 0
8
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6
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428
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DGE analysis with LIMMA
limma
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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0
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143
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Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
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3
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272
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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4
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277
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago mperalc • 0
3
votes
5
replies
605
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
votes
1
reply
246
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
vote
2
replies
282
views
Bioconductor unreachable?
limma
9 weeks ago edoardo • 0
0
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9
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535
views
limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
0
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2
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274
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limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
0
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2
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305
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Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 8 weeks ago alessandro • 0
2
votes
1
reply
282
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
1
vote
3
replies
334
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
0
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4
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346
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
3
votes
2
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275
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
2
votes
3
replies
310
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago • updated 10 weeks ago COPD_Project • 0
2
votes
2
replies
271
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
1
vote
4
replies
384
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 10
4
votes
3
replies
334
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
3
replies
353
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
1
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2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
2
replies
245
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
11 weeks ago Lily Cheang ▴ 10
1
vote
2
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321
views
Longitudinal analysis in Limma
limma
12 weeks ago COPD_Project • 0
2
votes
2
replies
269
views
Using limma for controlling age variable
linearmodeling limma
12 weeks ago Matej • 0
4
votes
6
replies
558
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
0
votes
5
replies
521
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
votes
4
replies
494
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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