Showing : limma • reset
1
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2
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84
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Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 2 hours ago Anna • 0
2
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2
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286
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
12 days ago • updated 7 days ago zzrammal • 0
3
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10
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483
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 13 days ago by • 0
5
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3
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318
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
1
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2
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283
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 days ago • updated 10 days ago Dylan.Sheerin • 0
3
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1
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1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 12 days ago by 50k • written 5.6 years ago by ▴ 10
1
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2
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409
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 16 days ago by 50k • written 16 days ago by • 0
0
votes
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 17 days ago by 50k • written 17 days ago by • 0
0
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2
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192
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 27 days ago by • 0
15
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17
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1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 18 days ago Chris ▴ 10
3
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4
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266
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Help with error using camera() in limma
CAMERA limma
20 days ago • updated 19 days ago Chris ▴ 10
2
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2
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1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 19 days ago by • 0 • written 8.0 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 19 days ago by • 0 • written 13.1 years ago by ▴ 10
0
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3
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282
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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 19 days ago by 65k • written 21 days ago by • 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
0
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7
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366
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 27 days ago hortense96 • 0
5
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8
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8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 27 days ago by • 0 • written 7.8 years ago by ▴ 30
0
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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
votes
9
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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
5
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9
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1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
0
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4
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634
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
1
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3
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369
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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469
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
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4
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332
views
Help with design.matrix
limma
6 weeks ago andrea.rodriguez-martinez13 • 0
0
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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
1
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4
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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
5
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25
replies
993
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
0
votes
2
replies
208
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks 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 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
2
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8
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568
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
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7
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493
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
0
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4
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416
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
9 weeks ago • updated 7 weeks ago Efra • 0
2
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6
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569
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 10
7
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6
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482
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Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
253
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
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2
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319
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
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3
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443
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
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8
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547
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
0
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3
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325
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
3
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5
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673
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
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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169
views
Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
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4
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328
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
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2
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350
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 12 weeks ago alessandro • 0
0
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9
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593
views
limma fo continous variables
limma DEGseq
updated 12 weeks ago by 65k • written 12 weeks ago by • 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
0
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4
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396
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 12 weeks ago Jitendra ▴ 10
1
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2
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350
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
votes
2
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322
views
limma model matrix questions
limmaGUI limma pairedsamples
3 months ago whyw6948 • 0
50 results • Page 1 of 1
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Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22 by James W. MacDonald 65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Votes
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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