Showing : limma • reset
0
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7
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244
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
8 days ago • updated 2 days ago hortense96 • 0
5
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8
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8.8k
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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
88
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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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152
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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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761
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Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by ★ 3.3k • written 5 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 5 days ago Chris • 0
3
votes
1
reply
117
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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
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9
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853
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Light difference when using coef vs omit a group when compare 3 groups.
limma
14 days ago • updated 7 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
567
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
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3
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320
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 10 days ago by 50k • written 15 days ago by • 0
2
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6
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345
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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
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290
views
Help with design.matrix
limma
19 days ago • updated 18 days ago andrea.rodriguez-martinez13 • 0
0
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1
reply
145
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 19 days ago by 50k • written 19 days ago by • 0
1
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4
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412
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by 50k • written 22 days ago by • 0
5
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25
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822
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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
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2
replies
171
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
22 days ago • updated 21 days ago Gimena • 0
0
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6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 23 days ago by 50k • written 9.8 years ago by ▴ 40
2
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8
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489
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 28 days ago by 50k • written 29 days ago by • 0
5
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7
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427
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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
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6
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445
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
7
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6
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430
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Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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1
reply
216
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
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2
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240
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
2
votes
2
replies
245
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
0
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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
481
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago • updated 6 weeks ago dl17032000 • 0
0
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3
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268
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
3
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5
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601
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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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426
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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
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142
views
Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
0
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4
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274
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago mperalc • 0
0
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2
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302
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
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limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
1
reply
244
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
0
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4
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341
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
1
vote
2
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279
views
Bioconductor unreachable?
limma
8 weeks ago edoardo • 0
0
votes
2
replies
273
views
limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
2
votes
1
reply
282
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
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379
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
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307
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago • updated 10 weeks ago COPD_Project • 0
3
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2
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274
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
4
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6
replies
557
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
269
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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334
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
352
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
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2
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242
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
11 weeks ago Lily Cheang ▴ 10
1
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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 ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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