Showing : Limma • reset
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 1 day ago by 50k • written 1 day ago by • 0
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2
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141
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 days ago • updated 1 day ago catv • 0
12
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12
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741
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Why p value inconsistent when using different number of pathway score?
limma
updated 2 days ago by ★ 3.3k • written 3 days ago by • 0
0
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1
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105
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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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233
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
6 days ago • updated 19 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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844
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Light difference when using coef vs omit a group when compare 3 groups.
limma
13 days ago • updated 5 days ago Chris • 0
2
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6
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336
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
15 days ago Chris • 0
0
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1
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143
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 17 days ago by 50k • written 18 days ago by • 0
0
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4
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288
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Help with design.matrix
limma
18 days ago • updated 17 days ago andrea.rodriguez-martinez13 • 0
1
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4
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409
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 19 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 Gimena • 0
15
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22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
25 days ago • updated 3 days ago Chris • 0
2
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8
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485
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 27 days ago by 50k • written 28 days ago by • 0
5
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25
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811
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 19 days ago by 50k • written 29 days ago by ▴ 10
7
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6
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429
views
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
views
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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367
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 29 days ago Efra • 0
5
votes
7
replies
426
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 27 days ago by 50k • written 5 weeks ago by • 0
2
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2
replies
243
views
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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234
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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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358
views
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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439
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 29 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
7 weeks ago • updated 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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267
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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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272
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago • updated 7 weeks ago mperalc • 0
3
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5
replies
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
242
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
vote
2
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273
views
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
views
limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
0
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2
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297
views
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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331
views
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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336
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
3
votes
2
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265
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
2
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3
replies
300
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 SamGG ▴ 350
1
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4
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371
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 10
4
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3
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326
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
replies
347
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
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2
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314
views
Longitudinal analysis in Limma
limma
12 weeks ago • updated 11 weeks ago COPD_Project • 0
2
votes
2
replies
264
views
Using limma for controlling age variable
linearmodeling limma
12 weeks ago Matej • 0
4
votes
6
replies
552
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
replies
511
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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486
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
Recent ...
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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