Showing : Limma • reset
14
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17
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1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
10 days ago • updated 10 hours ago Chris • 0
3
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4
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125
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Help with error using camera() in limma
CAMERA limma
21 hours ago • updated 17 hours ago Chris • 0
2
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2
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1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 18 hours ago by • 0 • written 7.9 years ago by • 0
0
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3
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1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 18 hours ago by • 0 • written 13.0 years ago by ▴ 10
0
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3
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183
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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 20 hours ago by 65k • written 1 day ago by • 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 21 hours ago Chris • 0
0
votes
7
replies
284
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
14 days ago • updated 8 days ago hortense96 • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 8 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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1
reply
128
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 8 days ago by 50k • written 8 days ago by • 0
0
votes
2
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188
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 days ago • updated 9 days ago catv • 0
3
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1
reply
153
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Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 13 days ago by • 0
5
votes
9
replies
892
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
20 days ago • updated 12 days ago Chris • 0
5
votes
9
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1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 13 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
588
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 14 days ago by 41k • written 6 months ago by • 0
1
vote
3
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337
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 16 days ago by 50k • written 21 days ago by • 0
2
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6
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378
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
22 days ago Chris • 0
0
votes
4
replies
298
views
Help with design.matrix
limma
25 days ago • updated 24 days ago andrea.rodriguez-martinez13 • 0
0
votes
1
reply
155
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 25 days ago by 50k • written 25 days ago by • 0
1
vote
4
replies
423
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 26 days ago by 50k • written 27 days ago by • 0
5
votes
25
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847
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 26 days ago by 50k • written 5 weeks ago by ▴ 10
0
votes
2
replies
180
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
28 days ago • updated 27 days ago Gimena • 0
0
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6
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3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 29 days ago by 50k • written 9.8 years ago by ▴ 40
2
votes
8
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511
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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7
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444
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DEG Filtering
MicroarrayData limma Genefiltering
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
383
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
6 weeks ago • updated 5 weeks ago Efra • 0
2
votes
6
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472
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
7
votes
6
replies
440
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
227
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
2
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257
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
2
votes
2
replies
253
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
1
vote
3
replies
392
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
3
votes
8
replies
493
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago • updated 7 weeks ago dl17032000 • 0
0
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3
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275
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
3
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5
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613
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
8
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6
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442
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
0
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147
views
Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
votes
4
replies
290
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago • updated 8 weeks ago mperalc • 0
0
votes
2
replies
310
views
Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 9 weeks ago alessandro • 0
0
votes
9
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545
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
2
votes
1
reply
255
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
votes
4
replies
360
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
1
vote
2
replies
297
views
Bioconductor unreachable?
limma
9 weeks ago edoardo • 0
0
votes
2
replies
280
views
limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
2
votes
1
reply
289
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
1
vote
3
replies
340
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 10
1
vote
4
replies
397
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
2
votes
3
replies
319
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago COPD_Project • 0
3
votes
2
replies
287
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
4
votes
6
replies
575
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
278
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
50 results • Page 1 of 1
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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