Showing : LIMMA • reset
1
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2
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88
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Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 5 hours ago Anna • 0
1
vote
2
replies
285
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 days ago • updated 10 days ago Dylan.Sheerin • 0
2
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2
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286
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 7 days ago zzrammal • 0
3
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10
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487
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 13 days ago by • 0
1
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2
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409
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 16 days ago by 50k • written 16 days ago by • 0
0
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1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 17 days ago by 50k • written 18 days ago by • 0
3
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4
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266
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Help with error using camera() in limma
CAMERA limma
20 days ago • updated 19 days ago Chris ▴ 10
0
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3
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282
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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 20 days ago by 65k • written 21 days ago by • 0
0
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2
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192
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 27 days ago by • 0
0
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2
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245
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 weeks ago • updated 28 days ago catv • 0
15
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17
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1.3k
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Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago Chris ▴ 10
5
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3
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319
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
0
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7
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366
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 27 days ago hortense96 • 0
1
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3
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369
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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9
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980
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Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
2
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6
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471
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
6 weeks ago • updated 5 weeks ago Chris ▴ 10
0
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1
reply
187
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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4
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332
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Help with design.matrix
limma
6 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
463
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
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2
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208
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
15
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23
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2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 20 days ago Chris ▴ 10
2
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8
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568
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
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25
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993
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
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6
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482
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
253
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
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4
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417
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
9 weeks ago • updated 7 weeks ago Efra • 0
5
votes
7
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493
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
2
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2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
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2
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320
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
1
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3
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443
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
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6
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572
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 10
3
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8
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547
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Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
8
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6
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509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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0
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170
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Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
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3
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325
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
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4
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328
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
3
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5
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673
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
votes
1
reply
281
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 weeks ago by 42k • written 12 weeks ago by ▴ 10
1
vote
2
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352
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
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9
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594
views
limma fo continous variables
limma DEGseq
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
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2
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322
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limma model matrix questions
limmaGUI limma pairedsamples
3 months ago whyw6948 • 0
0
votes
2
replies
351
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 12 weeks ago alessandro • 0
2
votes
1
reply
321
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
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3
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391
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 10
0
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4
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397
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 12 weeks ago Jitendra ▴ 10
3
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2
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322
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
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3
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352
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
2
votes
2
replies
307
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
1
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4
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447
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
4
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3
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385
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Comment: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm by Michael Love 42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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