Showing : limma • reset
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
19 hours ago Dylan.Sheerin • 0
1
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1
reply
103
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 2 days ago by 65k • written 2 days ago by • 0
1
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6
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177
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 1 day ago by ★ 3.3k • written 2 days ago by • 0
1
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2
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353
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 5 days ago by 50k • written 6 days ago by • 0
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1
reply
119
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Gene-by-sample covariates in limma
Metabolomics limma
updated 6 days ago by 50k • written 7 days ago by • 0
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4
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233
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Help with error using camera() in limma
CAMERA limma
9 days ago Chris • 0
0
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3
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252
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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 9 days ago by 65k • written 10 days ago by • 0
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2
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173
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 16 days ago by • 0
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2
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221
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
20 days ago • updated 17 days ago catv • 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
19 days ago • updated 8 days ago Chris • 0
3
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2
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223
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Log-cpm values from limma
limma edgeR RNASeq
21 days ago • updated 5 hours ago Shaimaa Gamal • 0
0
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7
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326
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
22 days ago • updated 16 days ago hortense96 • 0
1
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3
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353
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 24 days ago by 50k • written 29 days ago by • 0
5
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9
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936
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Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago Chris • 0
2
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6
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421
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
4 weeks ago Chris • 0
0
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1
reply
174
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
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4
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321
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Help with design.matrix
limma
4 weeks ago andrea.rodriguez-martinez13 • 0
1
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4
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447
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
0
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2
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197
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
5 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
5 weeks ago • updated 9 days ago Chris • 0
2
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8
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548
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
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25
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950
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
7
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6
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468
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
reply
237
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
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400
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
7 weeks ago • updated 6 weeks ago Efra • 0
5
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7
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466
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
2
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2
replies
269
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
0
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2
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283
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
8 weeks ago kcarey • 0
1
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3
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418
views
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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502
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
9 weeks ago • updated 6 weeks ago Lily Cheang ▴ 10
3
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8
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527
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Constrast for Time Course Experiments using Limma
limma
9 weeks ago dl17032000 • 0
8
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6
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473
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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3
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305
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
0
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4
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307
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago mperalc • 0
3
votes
5
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639
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
2
votes
1
reply
269
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
1
vote
2
replies
316
views
Bioconductor unreachable?
limma
11 weeks ago edoardo • 0
0
votes
9
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566
views
limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 11 weeks ago by • 0
0
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2
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299
views
limma model matrix questions
limmaGUI limma pairedsamples
11 weeks ago whyw6948 • 0
0
votes
2
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327
views
Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 10 weeks ago alessandro • 0
2
votes
1
reply
309
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
1
vote
3
replies
361
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
0
votes
4
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377
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 10 weeks ago Jitendra ▴ 10
3
votes
2
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302
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
votes
3
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332
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
2
votes
2
replies
293
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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419
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 3 months ago by ▴ 10
4
votes
3
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365
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
376
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Votes
Bioconductor 3.19 is Released!
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
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