Showing : Limma • reset
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
27 days ago • updated 5 days ago Chris • 0
12
votes
12
replies
781
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by ★ 3.3k • written 5 days ago by • 0
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
8
votes
6
replies
428
views
DGE analysis with LIMMA
limma
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
7
votes
6
replies
434
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
7
votes
2
replies
771
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
6
votes
5
replies
6.1k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
6
votes
7
replies
750
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 8 months ago by 50k • written 8 months ago by ▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 3 days ago by • 0 • written 7.7 years ago by ▴ 30
5
votes
25
replies
826
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 21 days ago by 50k • written 4 weeks ago by ▴ 10
5
votes
7
replies
430
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 29 days ago by 50k • written 5 weeks ago by • 0
5
votes
2
replies
673
views
PhD student
TMM limma
9 months ago Nisha • 0
5
votes
3
replies
692
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 6 months ago by 50k • written 6 months ago by ▴ 180
5
votes
9
replies
860
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
15 days ago • updated 7 days ago Chris • 0
5
votes
2
replies
536
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
5
votes
6
replies
3.7k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 days ago by 50k • written 7 months ago by ▴ 10
5
votes
8
replies
1.4k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
5
votes
5
replies
780
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
4
votes
6
replies
558
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
4
votes
3
replies
334
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
4
votes
5
replies
859
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by 50k • written 7 months ago by ▴ 10
4
votes
7
replies
2.0k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 8 months ago by 50k • written 7.9 years ago by • 0
3
votes
3
replies
561
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
3
votes
5
replies
861
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 17 months ago by • 0
3
votes
2
replies
438
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
11
replies
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago • updated 10 months ago Anna ▴ 20
3
votes
3
replies
1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
3
votes
2
replies
275
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
3
votes
1
reply
120
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
3
votes
13
replies
1.3k
views
Timely differentially expressed genes
timecoursedata limma
7 months ago • updated 4 months ago triZZla • 0
3
votes
4
replies
519
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
3
replies
913
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
3
votes
5
replies
605
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
3
votes
8
replies
482
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago dl17032000 • 0
3
votes
4
replies
701
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
3
votes
6
replies
832
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 7 months ago by 41k • written 2.9 years ago by • 0
2
votes
4
replies
613
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
2
votes
1
reply
246
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
3
replies
353
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
2
votes
1
reply
289
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
2
votes
8
replies
497
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 29 days ago by 50k • written 4 weeks ago by • 0
2
votes
4
replies
591
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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