Showing : limma • reset
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Gene-by-sample covariates in limma
Metabolomics limma
updated 3 hours ago by 50k • written 7 hours ago by • 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
0
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3
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209
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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
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
0
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2
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198
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
13 days ago • updated 10 days ago catv • 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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1
reply
163
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Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 14 days ago by • 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
1
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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
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
2
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6
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391
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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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1
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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
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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
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
0
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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
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
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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25
replies
881
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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
7
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6
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448
views
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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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
5
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7
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448
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
2
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2
replies
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
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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
1
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3
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397
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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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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
3
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8
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500
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Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
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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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
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
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
2
votes
1
reply
259
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 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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9
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553
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limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
0
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2
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287
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limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 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
2
votes
1
reply
292
views
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
vote
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
0
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4
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366
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
3
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2
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291
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
2
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3
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324
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Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago • updated 11 weeks ago COPD_Project • 0
2
votes
2
replies
284
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
1
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4
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404
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
4
votes
3
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348
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
2
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3
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364
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
2
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253
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
12 weeks ago Lily Cheang ▴ 10
1
vote
2
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337
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Longitudinal analysis in Limma
limma
3 months ago COPD_Project • 0
2
votes
2
replies
293
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Using limma for controlling age variable
linearmodeling limma
3 months ago Matej • 0
50 results • Page 1 of 1
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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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