Showing : limma • reset
1
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2
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307
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
1
reply
85
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 2 days ago by 50k • written 2 days ago by • 0
0
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2
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157
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 12 days ago by • 0
14
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17
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1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 3 days ago Chris • 0
3
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4
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193
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Help with error using camera() in limma
CAMERA limma
4 days ago Chris • 0
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 4 days 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 4 days ago by • 0 • written 13.0 years ago by ▴ 10
0
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3
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229
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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 4 days ago by 65k • written 5 days ago by • 0
15
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23
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2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 4 days ago Chris • 0
0
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7
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317
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
17 days ago • updated 11 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 11 days ago by • 0 • written 7.7 years ago by ▴ 30
0
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2
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210
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
15 days ago • updated 12 days ago catv • 0
3
votes
1
reply
173
views
Log-cpm values from limma
limma edgeR RNASeq
updated 15 days ago by 50k • written 16 days ago by • 0
5
votes
9
replies
923
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Light difference when using coef vs omit a group when compare 3 groups.
limma
24 days ago • updated 16 days ago Chris • 0
5
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9
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1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 17 days ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
600
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 18 days ago by 41k • written 6 months ago by • 0
1
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3
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347
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 24 days ago by • 0
2
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6
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398
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
26 days ago Chris • 0
0
votes
4
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307
views
Help with design.matrix
limma
29 days ago • updated 28 days ago andrea.rodriguez-martinez13 • 0
0
votes
1
reply
164
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 28 days ago by 50k • written 29 days ago by • 0
1
vote
4
replies
440
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
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25
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928
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 4 weeks ago by 50k • written 5 weeks ago by ▴ 10
0
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2
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189
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 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 4 weeks ago by 50k • written 9.8 years ago by ▴ 40
2
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8
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534
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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7
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454
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
replies
394
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
replies
486
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
7
votes
6
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453
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
1
reply
233
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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265
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
2
votes
2
replies
262
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
1
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3
replies
404
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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509
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
0
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3
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285
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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625
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 10 weeks ago by ▴ 10
8
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6
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456
views
DGE analysis with LIMMA
limma
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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0
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149
views
Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
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4
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299
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
0
votes
2
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317
views
Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 9 weeks ago alessandro • 0
0
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9
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560
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
1
reply
264
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
votes
4
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369
views
limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 9 weeks ago Jitendra ▴ 10
1
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2
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304
views
Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
votes
2
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292
views
limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
2
votes
1
reply
297
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
vote
3
replies
352
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 10
1
vote
4
replies
409
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
2
votes
3
replies
326
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago COPD_Project • 0
3
votes
2
replies
295
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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