Showing : limma • reset
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14
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Subsetting RNAseq data | voomaByGroup()
limma
12 hours ago Anna • 0
1
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2
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267
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
9 days ago • updated 8 days ago Dylan.Sheerin • 0
2
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2
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275
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 days ago • updated 5 days ago zzrammal • 0
3
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10
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451
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 8 days ago by 65k • written 11 days ago by • 0
1
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2
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403
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 14 days ago by 50k • written 15 days ago by • 0
0
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1
reply
155
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Gene-by-sample covariates in limma
Metabolomics limma
updated 16 days ago by 50k • written 16 days ago by • 0
3
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4
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261
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Help with error using camera() in limma
CAMERA limma
18 days ago Chris ▴ 10
0
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3
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274
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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 18 days ago by 65k • written 19 days ago by • 0
0
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2
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190
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 26 days ago by • 0
0
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2
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239
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
29 days ago • updated 26 days ago catv • 0
15
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17
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1.3k
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Why p value inconsistent when using different number of pathway score?
limma
28 days ago • updated 17 days ago Chris ▴ 10
5
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3
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307
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Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
0
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7
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363
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 25 days ago hortense96 • 0
1
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3
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369
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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9
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975
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Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
2
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6
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461
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
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1
reply
186
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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4
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331
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Help with design.matrix
limma
6 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
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463
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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207
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 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
7 weeks ago • updated 18 days ago Chris ▴ 10
2
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8
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564
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
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25
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990
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
7
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6
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481
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Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
252
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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4
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412
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
8 weeks ago • updated 7 weeks ago Efra • 0
5
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7
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487
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
2
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2
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289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
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2
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313
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
1
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3
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439
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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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560
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 10
3
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8
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540
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Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
8
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6
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504
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DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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0
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167
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Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
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3
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321
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
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4
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325
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
3
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5
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670
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
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1
reply
279
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
1
vote
2
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339
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Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
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9
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592
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limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
0
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2
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322
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limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
0
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2
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349
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 11 weeks ago alessandro • 0
2
votes
1
reply
320
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
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3
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388
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 10
0
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4
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394
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
3
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2
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319
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
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3
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349
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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
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306
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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441
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
4
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3
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380
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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
50 results • Page 1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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