Showing : limma • reset
3
votes
4
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163
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Help with error using camera() in limma
CAMERA limma
2 days ago • updated 1 day ago Chris • 0
0
votes
3
replies
202
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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 1 day ago by 65k • written 3 days ago by • 0
0
votes
2
replies
149
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 9 days ago by • 0
0
votes
2
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192
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
13 days ago • updated 10 days ago catv • 0
14
votes
17
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1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 21 hours ago Chris • 0
3
votes
1
reply
159
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Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 14 days ago by • 0
0
votes
7
replies
288
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
15 days ago • updated 9 days ago hortense96 • 0
1
vote
3
replies
342
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 17 days ago by 50k • written 22 days ago by • 0
5
votes
9
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896
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
21 days ago • updated 14 days ago Chris • 0
2
votes
6
replies
386
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
23 days ago Chris • 0
0
votes
1
reply
157
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 26 days ago by 50k • written 26 days ago by • 0
0
votes
4
replies
302
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Help with design.matrix
limma
26 days ago • updated 25 days ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
427
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 27 days ago by 50k • written 29 days ago by • 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
29 days ago • updated 28 days ago Gimena • 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago Chris • 0
2
votes
8
replies
517
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
25
replies
867
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 27 days ago by 50k • written 5 weeks ago by ▴ 10
7
votes
6
replies
446
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
231
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
4
replies
386
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
6 weeks ago • updated 5 weeks ago Efra • 0
5
votes
7
replies
447
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
replies
257
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
votes
2
replies
259
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
vote
3
replies
395
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
votes
6
replies
476
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
3
votes
8
replies
496
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
8
votes
6
replies
448
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
0
replies
148
views
Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
votes
3
replies
278
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
4
replies
294
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
3
votes
5
replies
615
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
2
votes
1
reply
259
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
1
vote
2
replies
300
views
Bioconductor unreachable?
limma
9 weeks ago edoardo • 0
0
votes
9
replies
550
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
2
replies
284
views
limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
0
votes
2
replies
312
views
Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 9 weeks ago alessandro • 0
2
votes
1
reply
290
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
replies
343
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 10
0
votes
4
replies
363
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
3
votes
2
replies
289
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
2
votes
3
replies
323
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
282
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
1
vote
4
replies
402
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
4
votes
3
replies
348
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
2
votes
3
replies
363
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
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
2
replies
252
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
12 weeks ago Lily Cheang ▴ 10
1
vote
2
replies
336
views
Longitudinal analysis in Limma
limma
3 months ago COPD_Project • 0
2
votes
2
replies
292
views
Using limma for controlling age variable
linearmodeling limma
3 months ago Matej • 0
4
votes
6
replies
581
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
50 results • Page 1 of 1
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Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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