Showing : LIMMA • reset
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66
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Gene-by-sample covariates in limma
Metabolomics limma
updated 17 hours ago by 50k • written 21 hours ago by • 0
3
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4
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174
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Help with error using camera() in limma
CAMERA limma
3 days ago • updated 2 days ago Chris • 0
0
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3
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214
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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 3 days ago by 65k • written 4 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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200
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
14 days ago • updated 11 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
13 days ago • updated 1 day ago Chris • 0
3
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1
reply
165
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Log-cpm values from limma
limma edgeR RNASeq
updated 14 days ago by 50k • written 15 days ago by • 0
0
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7
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299
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
16 days ago • updated 10 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 18 days ago by 50k • written 23 days ago by • 0
5
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9
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901
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Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 15 days ago Chris • 0
2
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6
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394
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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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159
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 27 days ago by 50k • written 27 days ago by • 0
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4
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304
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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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431
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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 4 weeks ago by • 0
0
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2
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184
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago • updated 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 3 days ago Chris • 0
2
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8
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521
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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
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886
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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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451
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
233
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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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4
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388
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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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449
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DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
2
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2
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259
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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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261
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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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401
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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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484
views
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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501
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Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
8
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6
replies
449
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 9 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
9 weeks ago Harrsha • 0
0
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3
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283
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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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622
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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
261
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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303
views
Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
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9
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557
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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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290
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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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315
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Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 9 weeks ago alessandro • 0
2
votes
1
reply
295
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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346
views
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
12 weeks ago • updated 9 weeks ago Jitendra ▴ 10
3
votes
2
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293
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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
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago • updated 11 weeks ago COPD_Project • 0
2
votes
2
replies
285
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
replies
405
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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
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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
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
1
vote
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
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2
replies
255
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
12 weeks ago Lily Cheang ▴ 10
1
vote
2
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340
views
Longitudinal analysis in Limma
limma
3 months ago COPD_Project • 0
2
votes
2
replies
294
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Using limma for controlling age variable
linearmodeling limma
3 months ago Matej • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
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…
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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