Showing : Limma • reset
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
20 days ago • updated 10 days ago Chris • 0
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 6 months ago by 50k • written 5.2 years ago by • 0
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
8
votes
6
replies
415
views
DGE analysis with LIMMA
limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
7
votes
6
replies
409
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 26 days ago by 50k • written 27 days ago by • 0
7
votes
2
replies
716
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
6.0k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
5
votes
7
replies
410
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 21 days ago by 50k • written 4 weeks ago by • 0
5
votes
5
replies
770
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
5
votes
6
replies
3.7k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 12 weeks ago by • 0 • written 3.1 years 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
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 19 hours ago by 50k • written 6 months ago by ▴ 10
5
votes
7
replies
736
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
3
replies
678
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
2
replies
507
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
2
replies
665
views
PhD student
TMM limma
9 months ago Nisha • 0
5
votes
25
replies
774
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 13 days ago by 50k • written 23 days ago by ▴ 10
5
votes
9
replies
778
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 6 hours ago Chris • 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 10 months ago by 50k • written 16 months ago by ▴ 20
4
votes
3
replies
313
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
4
votes
5
replies
851
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 6 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
4
votes
6
replies
538
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
votes
5
replies
846
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
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
3
votes
6
replies
813
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
2
replies
425
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
3
replies
555
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
4
replies
691
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
3
votes
3
replies
1.1k
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
13
replies
1.3k
views
Timely differentially expressed genes
timecoursedata limma
7 months ago • updated 4 months ago triZZla • 0
3
votes
2
replies
258
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 9 months ago by 50k • written 10 months ago by • 0
3
votes
5
replies
583
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
votes
3
replies
884
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
9 months ago amnahsiddiqa ▴ 10
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
4 months ago pl23 • 0
3
votes
8
replies
473
views
Constrast for Time Course Experiments using Limma
limma
6 weeks ago dl17032000 • 0
3
votes
11
replies
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
10 months ago Anna ▴ 20
2
votes
4
replies
1.1k
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
6
replies
303
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
10 days ago Chris • 0
2
votes
4
replies
593
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
5
replies
1.2k
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
329
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
1
reply
277
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
2
votes
1
reply
236
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
2
votes
2
replies
260
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
10 weeks ago SamGG ▴ 350
2
votes
1
reply
822
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 6 months ago by 50k • written 6 months ago by • 0
2
votes
4
replies
579
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
2
votes
8
replies
471
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 21 days ago by 50k • written 23 days ago by • 0
2
votes
6
replies
431
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 23 days ago Lily Cheang ▴ 10
50 results • Page 1 of 1
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Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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