Showing : limma • reset
1
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
1 day ago • updated 1 hour ago Dylan.Sheerin • 0
1
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1
reply
106
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 2 days ago by 65k • written 2 days ago by • 0
2
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9
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219
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Extremely small p-values using Limma for proteomic data
Proteomics limma
2 days ago • updated 4 hours ago Abbey • 0
1
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2
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353
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 6 days ago by 50k • written 6 days ago by • 0
0
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1
reply
120
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Gene-by-sample covariates in limma
Metabolomics limma
updated 7 days ago by 50k • written 7 days ago by • 0
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4
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233
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Help with error using camera() in limma
CAMERA limma
9 days ago Chris • 0
0
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3
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253
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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 9 days ago by 65k • written 10 days ago by • 0
0
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2
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173
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 17 days ago by • 0
0
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2
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221
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
20 days ago • updated 17 days ago catv • 0
14
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17
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1.2k
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Why p value inconsistent when using different number of pathway score?
limma
19 days ago • updated 8 days ago Chris • 0
3
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3
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239
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 hours ago by 50k • written 21 days ago by • 0
0
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7
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326
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
22 days ago • updated 16 days ago hortense96 • 0
1
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3
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353
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 24 days ago by 50k • written 29 days ago by • 0
5
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9
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937
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Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago Chris • 0
2
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6
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424
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
4 weeks ago Chris • 0
0
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1
reply
174
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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4
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321
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Help with design.matrix
limma
4 weeks ago andrea.rodriguez-martinez13 • 0
1
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4
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447
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
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2
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197
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
5 weeks ago Gimena • 0
15
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23
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2.0k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 9 days ago Chris • 0
2
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8
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548
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
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25
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954
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 10
7
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6
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468
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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1
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237
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
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400
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Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
7 weeks ago • updated 6 weeks ago Efra • 0
5
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7
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467
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
2
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2
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270
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
0
votes
2
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283
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 weeks ago kcarey • 0
1
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3
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418
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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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502
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
9 weeks ago • updated 6 weeks ago Lily Cheang ▴ 10
3
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8
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527
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Constrast for Time Course Experiments using Limma
limma
9 weeks ago dl17032000 • 0
8
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6
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476
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DGE analysis with LIMMA
limma
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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0
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155
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Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
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3
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306
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
0
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4
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307
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago mperalc • 0
3
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5
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639
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
2
votes
1
reply
270
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
1
vote
2
replies
316
views
Bioconductor unreachable?
limma
11 weeks ago edoardo • 0
0
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9
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567
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limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 11 weeks ago by • 0
0
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2
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299
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limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
0
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2
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328
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Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 10 weeks ago alessandro • 0
2
votes
1
reply
309
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
1
vote
3
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361
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
0
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4
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377
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 10 weeks ago Jitendra ▴ 10
3
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2
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303
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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334
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Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
2
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2
replies
293
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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419
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 3 months ago by ▴ 10
4
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3
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365
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
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3
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376
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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Replies
Comment: deseq2 results by swbarnes2 ★ 1.3k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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