Showing : limma • reset
0
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101
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 4 days ago by 50k • written 4 days ago by • 0
0
votes
2
replies
163
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 days ago • updated 5 days ago catv • 0
12
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12
replies
801
views
Why p value inconsistent when using different number of pathway score?
limma
updated 5 days ago by ★ 3.3k • written 6 days ago by • 0
3
votes
1
reply
124
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 9 days ago by • 0
0
votes
7
replies
258
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
10 days ago • updated 4 days ago hortense96 • 0
1
vote
3
replies
327
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 12 days ago by 50k • written 17 days ago by • 0
5
votes
9
replies
866
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
16 days ago • updated 8 days ago Chris • 0
2
votes
6
replies
355
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
18 days ago Chris • 0
0
votes
1
reply
149
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 21 days ago by 50k • written 21 days ago by • 0
0
votes
4
replies
291
views
Help with design.matrix
limma
21 days ago • updated 20 days ago andrea.rodriguez-martinez13 • 0
1
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4
replies
417
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 22 days ago by 50k • written 23 days ago by • 0
0
votes
2
replies
174
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
24 days ago • updated 23 days ago Gimena • 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
28 days ago • updated 6 days ago Chris • 0
2
votes
8
replies
504
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
votes
25
replies
830
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 22 days ago by 50k • written 4 weeks ago by ▴ 10
7
votes
6
replies
436
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
220
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
4
replies
375
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 4 weeks ago Efra • 0
5
votes
7
replies
434
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
249
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
0
votes
2
replies
247
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
vote
3
replies
383
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
2
votes
6
replies
455
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
3
votes
8
replies
482
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago dl17032000 • 0
8
votes
6
replies
429
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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0
replies
144
views
Can I combine collinear variables into a single value
BatchEffect limma
8 weeks ago Harrsha • 0
0
votes
3
replies
272
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
4
replies
281
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago mperalc • 0
3
votes
5
replies
606
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 9 weeks ago by ▴ 10
2
votes
1
reply
248
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
vote
2
replies
285
views
Bioconductor unreachable?
limma
9 weeks ago edoardo • 0
0
votes
9
replies
536
views
limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
0
votes
2
replies
275
views
limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
0
votes
2
replies
306
views
Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 8 weeks ago alessandro • 0
2
votes
1
reply
283
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
1
vote
3
replies
336
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
0
votes
4
replies
347
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 8 weeks ago Jitendra ▴ 10
3
votes
2
replies
276
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
2
votes
3
replies
311
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago COPD_Project • 0
2
votes
2
replies
273
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
1
vote
4
replies
387
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 10
4
votes
3
replies
337
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
3
replies
355
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
2
replies
245
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
11 weeks ago Lily Cheang ▴ 10
1
vote
2
replies
324
views
Longitudinal analysis in Limma
limma
12 weeks ago COPD_Project • 0
2
votes
2
replies
274
views
Using limma for controlling age variable
linearmodeling limma
12 weeks ago Matej • 0
4
votes
6
replies
564
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
0
votes
5
replies
522
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
498
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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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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