Showing : limma • reset
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 14 hours ago by 50k • written 15 hours ago by • 0
0
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2
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135
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
3 days ago • updated 1 day ago catv • 0
12
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12
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719
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Why p value inconsistent when using different number of pathway score?
limma
updated 1 day ago by ★ 3.3k • written 3 days ago by • 0
0
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1
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103
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 days ago by 50k • written 5 days ago by • 0
0
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7
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225
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
6 days ago • updated 5 hours ago hortense96 • 0
1
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3
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317
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 8 days ago by 50k • written 13 days ago by • 0
5
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9
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841
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Light difference when using coef vs omit a group when compare 3 groups.
limma
12 days ago • updated 5 days ago Chris • 0
2
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6
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334
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
14 days ago Chris • 0
0
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1
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143
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 17 days ago by 50k • written 17 days ago by • 0
0
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4
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288
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Help with design.matrix
limma
17 days ago • updated 16 days ago andrea.rodriguez-martinez13 • 0
1
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4
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406
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 18 days ago by 50k • written 20 days ago by • 0
0
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2
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166
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
20 days ago • updated 19 days ago Gimena • 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
24 days ago • updated 3 days ago Chris • 0
2
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8
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484
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 26 days ago by 50k • written 27 days ago by • 0
5
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25
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805
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 18 days ago by 50k • written 28 days ago by ▴ 10
7
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6
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428
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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
214
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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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4
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366
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Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 28 days ago Efra • 0
5
votes
7
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424
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DEG Filtering
MicroarrayData limma Genefiltering
updated 26 days ago by 50k • written 5 weeks ago by • 0
2
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2
replies
243
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
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2
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233
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
0
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3
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357
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
2
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6
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438
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 28 days ago Lily Cheang ▴ 10
3
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8
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480
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Constrast for Time Course Experiments using Limma
limma
6 weeks ago dl17032000 • 0
8
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6
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425
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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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140
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Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
0
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3
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266
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
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4
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271
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago mperalc • 0
3
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5
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597
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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1
reply
241
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
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2
replies
270
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Bioconductor unreachable?
limma
8 weeks ago edoardo • 0
0
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9
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520
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limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
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2
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269
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limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
0
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2
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297
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Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 8 weeks ago alessandro • 0
2
votes
1
reply
278
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
1
vote
3
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330
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
0
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4
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333
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limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
3
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2
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265
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
2
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3
replies
299
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
10 weeks ago COPD_Project • 0
2
votes
2
replies
266
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago • updated 10 weeks ago SamGG ▴ 350
1
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4
replies
367
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
4
votes
3
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325
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
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3
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344
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months 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
vote
2
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313
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Longitudinal analysis in Limma
limma
11 weeks ago COPD_Project • 0
2
votes
2
replies
263
views
Using limma for controlling age variable
linearmodeling limma
12 weeks ago Matej • 0
4
votes
6
replies
549
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
0
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5
replies
509
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
votes
4
replies
482
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Votes
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
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