Showing : limma • reset
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 19 days ago Chris ▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 18 days ago Chris ▴ 10
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.3 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
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
7
votes
2
replies
866
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
7
votes
6
replies
482
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
6
votes
5
replies
6.4k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
6
votes
7
replies
798
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
5
votes
5
replies
827
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 10
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 27 days ago by • 0 • written 7.8 years ago by ▴ 30
5
votes
3
replies
317
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
5
votes
2
replies
703
views
PhD student
TMM limma
10 months ago Nisha • 0
5
votes
2
replies
607
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
5
votes
25
replies
993
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
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 5 months ago by • 0 • written 12 months ago by ▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
5
votes
3
replies
723
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 7 months ago by 50k • written 7 months ago by ▴ 180
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
4
votes
8
replies
2.2k
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
6
replies
653
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
4
votes
3
replies
385
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
5
replies
893
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by 50k • written 8 months ago by ▴ 10
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
2
replies
322
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata limma
8 months ago • updated 5 months ago triZZla • 0
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
8 months ago Ethan Nguyen • 0
3
votes
3
replies
595
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 8 months ago by 65k • written 8 months ago by • 0
3
votes
3
replies
989
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
4
replies
563
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
10
replies
482
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 12 days ago by • 0
3
votes
8
replies
545
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
3
votes
11
replies
2.6k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
12 months ago • updated 11 months ago Anna ▴ 20
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 12 days ago by 50k • written 5.6 years ago by ▴ 10
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 11 months ago by 50k • written 11 months ago by • 0
3
votes
5
replies
932
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 4 months ago by ▴ 30 • written 18 months ago by • 0
3
votes
2
replies
465
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
5
replies
673
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
votes
6
replies
862
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
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA limma
19 days ago Chris ▴ 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 9 months ago by 65k • written 9 months ago by ▴ 10
2
votes
2
replies
306
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago SamGG ▴ 350
2
votes
1
reply
314
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 5 months ago by 50k • written 5 months ago by • 0
2
votes
1
reply
281
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
votes
8
replies
568
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
1
reply
880
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
Votes
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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