Showing : limma • reset
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Gene-by-sample covariates in limma
Metabolomics limma
updated 1 hour ago by 50k • written 6 hours ago by • 0
0
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2
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150
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 days ago by • 0
14
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17
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1.1k
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Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago Chris • 0
3
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4
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166
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Help with error using camera() in limma
CAMERA limma
2 days ago Chris • 0
2
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2
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1.0k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 2 days ago by • 0 • written 7.9 years ago by • 0
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3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 2 days ago by • 0 • written 13.0 years ago by ▴ 10
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3
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208
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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 2 days ago by 65k • written 3 days ago by • 0
15
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23
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1.9k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago Chris • 0
0
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7
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292
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
15 days ago • updated 9 days ago hortense96 • 0
5
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8
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8.8k
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 9 days ago by • 0 • written 7.7 years ago by ▴ 30
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2
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196
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
13 days ago • updated 10 days ago catv • 0
3
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1
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161
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Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 14 days ago by • 0
5
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9
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899
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Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago Chris • 0
5
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9
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1.2k
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Batch correction and repeated measures
RUVSeq sva limma
updated 14 days ago by 50k • written 7 months ago by ▴ 10
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4
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592
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
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3
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343
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 17 days ago by 50k • written 22 days ago by • 0
2
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6
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389
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
24 days ago Chris • 0
0
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4
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302
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Help with design.matrix
limma
27 days ago • updated 26 days ago andrea.rodriguez-martinez13 • 0
0
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1
reply
157
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 26 days ago by 50k • written 27 days ago by • 0
1
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4
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428
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 28 days ago by 50k • written 29 days ago by • 0
5
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25
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877
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 28 days ago by 50k • written 5 weeks ago by ▴ 10
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2
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183
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
29 days ago Gimena • 0
0
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6
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3.1k
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limma, analysis on subset of data gives completely different results
limma limma
updated 4 weeks ago by 50k • written 9.8 years ago by ▴ 40
2
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8
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519
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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7
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448
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DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
0
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4
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387
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Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
6 weeks ago • updated 5 weeks ago Efra • 0
2
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6
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481
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
7
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6
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448
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Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
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1
reply
231
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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259
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
2
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2
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257
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
1
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3
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396
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
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8
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498
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
0
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3
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280
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
3
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5
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615
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
8
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6
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449
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DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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0
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148
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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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4
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296
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
0
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2
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314
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Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 9 weeks ago alessandro • 0
0
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9
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552
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limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
2
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1
reply
259
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
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4
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364
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limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
1
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2
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300
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Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
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2
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286
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limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
2
votes
1
reply
292
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
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3
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345
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 10
1
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4
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404
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
2
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3
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324
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago • updated 11 weeks ago COPD_Project • 0
3
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2
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290
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
4
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6
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586
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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