Showing : LIMMA • reset
1
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2
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95
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 18 hours ago Anna • 0
1
vote
2
replies
288
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 days ago • updated 11 days ago Dylan.Sheerin • 0
2
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2
replies
286
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 8 days ago zzrammal • 0
3
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10
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493
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 66k • written 13 days ago by • 0
1
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2
replies
409
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 days ago by 50k • written 17 days ago by • 0
0
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1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 18 days ago by 50k • written 18 days ago by • 0
3
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4
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267
views
Help with error using camera() in limma
CAMERA limma
20 days ago Chris ▴ 10
0
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3
replies
283
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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 days ago by 66k • written 21 days ago by • 0
0
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2
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192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 28 days ago by • 0
15
votes
17
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1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago Chris ▴ 10
0
votes
2
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245
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 weeks ago • updated 28 days ago catv • 0
5
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3
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320
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 4 weeks ago by • 0
0
votes
7
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369
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 27 days ago hortense96 • 0
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
1
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3
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370
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
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6
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474
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
6 weeks ago Chris ▴ 10
0
votes
1
reply
187
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
333
views
Help with design.matrix
limma
6 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
463
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
2
replies
209
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
15
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23
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2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 20 days ago Chris ▴ 10
2
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8
replies
568
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
25
replies
995
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 8 weeks ago by ▴ 10
7
votes
6
replies
487
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
1
reply
256
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
4
replies
418
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
9 weeks ago • updated 8 weeks ago Efra • 0
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
replies
291
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
votes
2
replies
320
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
2
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6
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575
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 8 weeks ago Lily Cheang ▴ 10
3
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8
replies
548
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
8
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6
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509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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0
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170
views
Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
votes
3
replies
326
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
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4
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329
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
2
votes
1
reply
281
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
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5
replies
673
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
1
vote
2
replies
355
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
votes
9
replies
595
views
limma fo continous variables
limma DEGseq
updated 12 weeks ago by 66k • written 12 weeks ago by • 0
0
votes
2
replies
322
views
limma model matrix questions
limmaGUI limma pairedsamples
3 months ago whyw6948 • 0
0
votes
2
replies
352
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 12 weeks ago alessandro • 0
2
votes
1
reply
321
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
3
replies
391
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 10
0
votes
4
replies
397
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 12 weeks ago Jitendra ▴ 10
3
votes
2
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323
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
votes
3
replies
352
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
1
vote
4
replies
448
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
2
votes
2
replies
307
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
4
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3
replies
385
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
392
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
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