Showing : Limma • reset
1
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 hours ago by ★ 3.3k • written 1 day ago by • 0
3
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1
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1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 15 hours ago by 50k • written 5.6 years ago by ▴ 10
1
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1
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81
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 1 day ago by 65k • written 1 day ago by • 0
1
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2
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343
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 4 days ago by 50k • written 4 days ago by • 0
0
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1
reply
111
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Gene-by-sample covariates in limma
Metabolomics limma
updated 5 days ago by 50k • written 6 days ago by • 0
0
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2
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172
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 15 days ago by • 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
18 days ago • updated 7 days ago Chris • 0
3
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4
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224
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Help with error using camera() in limma
CAMERA limma
8 days ago • updated 7 days ago Chris • 0
2
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2
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1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 8 days ago by • 0 • written 7.9 years ago by • 0
0
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3
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1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 8 days ago by • 0 • written 13.0 years ago by ▴ 10
0
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3
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248
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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 8 days ago by 65k • written 9 days ago by • 0
15
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23
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2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 8 days ago Chris • 0
0
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7
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325
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
21 days ago • updated 15 days ago hortense96 • 0
5
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8
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8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 15 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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2
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215
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
19 days ago • updated 16 days ago catv • 0
3
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1
reply
180
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Log-cpm values from limma
limma edgeR RNASeq
updated 19 days ago by 50k • written 20 days ago by • 0
5
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9
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934
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Light difference when using coef vs omit a group when compare 3 groups.
limma
27 days ago • updated 20 days ago Chris • 0
5
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9
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1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 22 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 23 days ago by 50k • written 28 days ago by • 0
2
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6
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411
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
4 weeks ago • updated 29 days ago Chris • 0
0
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4
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318
views
Help with design.matrix
limma
4 weeks ago andrea.rodriguez-martinez13 • 0
0
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1
reply
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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445
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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25
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943
views
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
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
5 weeks ago Gimena • 0
0
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6
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3.1k
views
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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8
replies
544
views
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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465
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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
views
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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496
views
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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462
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
views
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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280
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
2
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2
replies
266
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
1
vote
3
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414
views
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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524
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago • updated 8 weeks ago dl17032000 • 0
0
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3
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300
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
3
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5
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638
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
8
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6
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468
views
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
views
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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305
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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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324
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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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565
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limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
1
reply
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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376
views
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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313
views
Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
votes
2
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298
views
limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
2
votes
1
reply
305
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
1
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3
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360
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
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
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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