Showing : limma • reset
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 20 minutes ago by 65k • written 1 hour ago by • 0
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25
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 1 hour ago by 65k • written 2 hours ago by • 0
1
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2
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336
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 3 days ago by 50k • written 3 days ago by • 0
0
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108
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Gene-by-sample covariates in limma
Metabolomics limma
updated 4 days ago by 50k • written 4 days ago by • 0
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 14 days ago by • 0
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Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 5 days ago Chris • 0
3
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Help with error using camera() in limma
CAMERA limma
7 days ago • updated 6 days ago Chris • 0
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1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 6 days ago by • 0 • written 7.9 years ago by • 0
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 6 days ago by • 0 • written 13.0 years ago by ▴ 10
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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 7 days ago by 65k • written 8 days ago by • 0
15
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 7 days ago Chris • 0
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7
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
20 days ago • updated 14 days ago hortense96 • 0
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 14 days ago by • 0 • written 7.7 years ago by ▴ 30
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
18 days ago • updated 15 days ago catv • 0
3
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179
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Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
5
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9
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931
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Light difference when using coef vs omit a group when compare 3 groups.
limma
26 days ago • updated 19 days ago Chris • 0
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1.3k
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Batch correction and repeated measures
RUVSeq sva limma
updated 19 days ago by 50k • written 7 months ago by ▴ 10
0
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4
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603
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 days ago by 42k • written 6 months ago by • 0
1
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3
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352
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 22 days ago by 50k • written 27 days ago by • 0
2
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6
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405
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
29 days ago • updated 28 days ago Chris • 0
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4
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315
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Help with design.matrix
limma
4 weeks ago andrea.rodriguez-martinez13 • 0
0
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1
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171
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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
1
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4
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444
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
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25
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939
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 4 weeks ago by 50k • written 6 weeks ago by ▴ 10
0
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2
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195
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks 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 5 weeks ago by 50k • written 9.8 years ago by ▴ 40
2
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
5
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7
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461
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DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
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399
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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
2
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6
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492
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 6 weeks ago Lily Cheang ▴ 10
7
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6
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459
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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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236
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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273
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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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266
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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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412
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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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519
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Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
0
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3
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294
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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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633
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
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6
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463
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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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153
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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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4
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304
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago • updated 9 weeks ago mperalc • 0
0
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2
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323
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Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 10 weeks ago alessandro • 0
0
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9
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564
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limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
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1
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267
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
0
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4
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375
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limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 10 weeks ago Jitendra ▴ 10
1
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2
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312
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Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
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2
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297
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limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
2
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1
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305
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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
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3
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359
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
1
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4
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415
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 3 months ago by ▴ 10
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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