Showing : limma • reset
1
vote
2
replies
255
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
9 days ago • updated 8 days ago Dylan.Sheerin • 0
2
votes
2
replies
269
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 4 days ago zzrammal • 0
3
votes
10
replies
441
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 7 days ago by 65k • written 10 days ago by • 0
1
vote
2
replies
398
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 15 days ago by 50k • written 15 days ago by • 0
3
votes
4
replies
260
views
Help with error using camera() in limma
CAMERA limma
17 days ago Chris ▴ 10
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 17 days ago by 65k • written 18 days ago by • 0
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 25 days ago by • 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
28 days ago • updated 25 days ago catv • 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago Chris ▴ 10
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 29 days ago by • 0
0
votes
7
replies
362
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 24 days ago hortense96 • 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
9
replies
974
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 29 days ago Chris ▴ 10
2
votes
6
replies
459
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
votes
1
reply
185
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
330
views
Help with design.matrix
limma
6 weeks ago • updated 5 weeks ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
462
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
2
replies
207
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 17 days ago Chris ▴ 10
2
votes
8
replies
560
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
25
replies
986
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
7
votes
6
replies
481
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
1
reply
250
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
4
replies
410
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
8 weeks ago • updated 7 weeks ago Efra • 0
5
votes
7
replies
484
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
votes
2
replies
313
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
1
vote
3
replies
439
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
votes
6
replies
556
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 10
3
votes
8
replies
540
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
8
votes
6
replies
502
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
0
replies
165
views
Can I combine collinear variables into a single value
BatchEffect limma
11 weeks ago Harrsha • 0
0
votes
3
replies
318
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
4
replies
323
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
3
votes
5
replies
668
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
votes
1
reply
278
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
1
vote
2
replies
338
views
Bioconductor unreachable?
limma
12 weeks ago edoardo • 0
0
votes
9
replies
589
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
2
replies
318
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
0
votes
2
replies
347
views
Limma with replicates at different time points
RNAs limma Differen
3 months ago • updated 11 weeks ago alessandro • 0
2
votes
1
reply
320
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
3
replies
386
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 3 months ago by 50k • written 3 months ago by ▴ 10
0
votes
4
replies
393
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
3
votes
2
replies
317
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
votes
3
replies
348
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
3 months ago COPD_Project • 0
2
votes
2
replies
305
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
1
vote
4
replies
441
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 3 months ago by 50k • written 3 months ago by ▴ 10
4
votes
3
replies
378
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
India, 9 minutes ago
The city by the bay, 13 minutes ago
United States, 25 minutes ago
410 Lawrence Bell Dr suite 1, Buffalo, NY 14221, United States, 30 minutes ago
Italy, 40 minutes ago
Traffic: 440 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6