Showing : limma • reset
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
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
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata limma
8 months ago • updated 5 months ago triZZla • 0
1
vote
12
replies
2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 3 months ago by • 0 • written 2.6 years ago by ▴ 380
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
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
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
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
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
0
votes
9
replies
593
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
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
3
votes
8
replies
545
views
Constrast for Time Course Experiments using Limma
limma
10 weeks ago dl17032000 • 0
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
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
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
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
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
5
votes
7
replies
493
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
1
vote
7
replies
884
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
0
votes
7
replies
366
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 27 days ago hortense96 • 0
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
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
8
votes
6
replies
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
6
replies
872
views
Help with model.matrix and creating the right contrast matrix for limma
limma
8 months ago • updated 5 months ago rober204 • 0
2
votes
6
replies
568
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 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
0
votes
6
replies
812
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
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
1
vote
6
replies
954
views
Limma dispersed distribution of log fold change
limma
written 8 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
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
2
votes
6
replies
468
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.7 years ago by ▴ 20
0
votes
5
replies
835
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 5 months ago by 50k • written 7 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
0
votes
5
replies
975
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
7 months ago dorota.komar • 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
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
1
vote
5
replies
1.1k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 10 months ago by 50k • written 10 months ago by • 0
0
votes
5
replies
1.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 14 months ago by • 0
0
votes
5
replies
612
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months 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
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
5
votes
5
replies
827
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
1
vote
4
replies
663
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
4
replies
396
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 12 weeks ago Jitendra ▴ 10
1
vote
4
replies
748
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
0
votes
4
replies
634
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
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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