Showing : Limma • reset
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
updated 7 hours ago by 50k • written 15 hours ago by • 0
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1
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67
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Log-cpm values from limma
limma edgeR RNASeq
updated 21 hours ago by 50k • written 1 day ago by • 0
0
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6
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158
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
updated 2 days ago by 50k • written 2 days ago by • 0
1
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3
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309
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 days ago by 50k • written 9 days ago by • 0
5
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9
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807
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Light difference when using coef vs omit a group when compare 3 groups.
limma
9 days ago • updated 1 day ago Chris • 0
2
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6
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310
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
11 days ago Chris • 0
0
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1
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140
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 13 days ago by 50k • written 14 days ago by • 0
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4
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281
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Help with design.matrix
limma
14 days ago • updated 13 days ago andrea.rodriguez-martinez13 • 0
1
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4
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399
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 15 days ago by 50k • written 16 days ago by • 0
0
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2
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162
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
16 days ago Gimena • 0
14
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20
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1.7k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 8 hours ago Chris • 0
2
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8
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475
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 23 days ago by 50k • written 24 days ago by • 0
5
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25
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790
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 15 days ago by 50k • written 25 days ago by ▴ 10
7
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6
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412
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Batch Effect Correction, Gene Filtering
DGE limma
updated 28 days ago by 50k • written 28 days ago by • 0
0
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1
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206
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 29 days ago by 50k • written 29 days ago by • 0
0
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4
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361
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Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
4 weeks ago • updated 25 days ago Efra • 0
5
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7
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415
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DEG Filtering
MicroarrayData limma Genefiltering
updated 23 days ago by 50k • written 4 weeks ago by • 0
2
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2
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239
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
0
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2
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227
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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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354
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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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436
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 25 days ago Lily Cheang ▴ 10
3
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8
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477
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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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419
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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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138
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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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264
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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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263
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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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589
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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1
reply
238
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
1
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2
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266
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Bioconductor unreachable?
limma
8 weeks ago edoardo • 0
0
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9
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508
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limma fo continous variables
limma DEGseq
updated 7 weeks ago by 65k • written 8 weeks ago by • 0
0
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2
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265
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limma model matrix questions
limmaGUI limma pairedsamples
8 weeks ago whyw6948 • 0
0
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2
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292
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Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 7 weeks ago alessandro • 0
2
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1
reply
275
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
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3
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327
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 10
0
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4
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325
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limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 7 weeks ago Jitendra ▴ 10
3
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2
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259
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
2
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3
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290
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Longitudinal analysis in Limma: Block=ID as random effect
limma
10 weeks ago COPD_Project • 0
2
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2
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263
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
10 weeks ago SamGG ▴ 350
1
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4
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353
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 9 weeks ago by 50k • written 10 weeks ago by ▴ 10
4
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3
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317
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
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3
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335
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 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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238
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
10 weeks ago Lily Cheang ▴ 10
1
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2
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308
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Longitudinal analysis in Limma
limma
11 weeks ago COPD_Project • 0
2
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2
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259
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Using limma for controlling age variable
linearmodeling limma
11 weeks ago Matej • 0
4
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6
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541
views
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
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497
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
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474
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
1
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2
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448
views
Assess fit of variance prior
limma
updated 4 months ago by 50k • written 4 months ago by ▴ 20
2
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1
reply
281
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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