Showing : Limma • reset
0
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7
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239
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
7 days ago • updated 2 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 2 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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1
reply
87
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 2 days ago by 50k • written 2 days ago by • 0
0
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2
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151
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 days ago • updated 3 days ago catv • 0
12
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12
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755
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Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by ★ 3.3k • written 4 days ago by • 0
15
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22
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1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago Chris • 0
3
votes
1
reply
115
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Log-cpm values from limma
limma edgeR RNASeq
updated 6 days ago by 50k • written 7 days ago by • 0
5
votes
9
replies
853
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
14 days ago • updated 6 days ago Chris • 0
5
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9
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1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 7 days ago by 50k • written 7 months ago by ▴ 10
0
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4
replies
565
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 days ago by 41k • written 6 months ago by • 0
1
vote
3
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320
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 9 days ago by 50k • written 15 days ago by • 0
2
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6
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343
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
16 days ago Chris • 0
0
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4
replies
289
views
Help with design.matrix
limma
19 days ago • updated 18 days ago andrea.rodriguez-martinez13 • 0
0
votes
1
reply
144
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 19 days ago by 50k • written 19 days ago by • 0
1
vote
4
replies
412
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by 50k • written 21 days ago by • 0
5
votes
25
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818
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 20 days ago by 50k • written 4 weeks ago by ▴ 10
0
votes
2
replies
169
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
22 days ago • updated 21 days ago Gimena • 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 22 days ago by 50k • written 9.8 years ago by ▴ 40
2
votes
8
replies
486
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 28 days ago by 50k • written 29 days ago by • 0
5
votes
7
replies
427
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 28 days ago by 50k • written 5 weeks ago by • 0
0
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4
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369
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 4 weeks ago Efra • 0
2
votes
6
replies
443
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
7
votes
6
replies
430
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
1
reply
214
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
2
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236
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
2
votes
2
replies
244
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago • updated 5 weeks ago Sabiha ▴ 20
0
votes
3
replies
359
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
3
votes
8
replies
480
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago • updated 6 weeks ago dl17032000 • 0
0
votes
3
replies
268
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
3
votes
5
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600
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
8
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6
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425
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DGE analysis with LIMMA
limma
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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0
replies
141
views
Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
0
votes
4
replies
273
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago • updated 7 weeks ago mperalc • 0
0
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2
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301
views
Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 8 weeks ago alessandro • 0
0
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9
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530
views
limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
1
reply
243
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
0
votes
4
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340
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
1
vote
2
replies
278
views
Bioconductor unreachable?
limma
8 weeks ago edoardo • 0
0
votes
2
replies
271
views
limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
2
votes
1
reply
280
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
1
vote
3
replies
332
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
1
vote
4
replies
378
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 10
2
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3
replies
305
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago • updated 10 weeks ago COPD_Project • 0
3
votes
2
replies
272
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago • updated 10 weeks ago Shaimaa Gamal • 0
4
votes
6
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555
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
2
votes
2
replies
268
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
4
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3
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333
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
3
replies
351
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
2
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242
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
11 weeks ago Lily Cheang ▴ 10
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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