Showing : LIMMA • reset
5
votes
25
replies
882
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 28 days ago by 50k • written 5 weeks ago by ▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago Chris • 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago Chris • 0
3
votes
13
replies
1.4k
views
Timely differentially expressed genes
timecoursedata limma
7 months ago • updated 5 months ago triZZla • 0
1
vote
12
replies
2.4k
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 2.5 years ago by ▴ 380
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
11
replies
2.5k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago Anna ▴ 20
0
votes
9
replies
554
views
limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 15 days ago by 50k • written 7 months ago by ▴ 10
5
votes
9
replies
899
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago Chris • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 9 days ago by • 0 • written 7.7 years ago by ▴ 30
5
votes
8
replies
1.5k
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
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
3
votes
8
replies
501
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
2
votes
8
replies
519
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
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 7.9 years ago by • 0
1
vote
7
replies
829
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 6 months ago by • 0
5
votes
7
replies
449
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
7
replies
294
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
15 days ago • updated 9 days ago hortense96 • 0
0
votes
7
replies
1.4k
views
A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
6
votes
7
replies
760
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
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 4 weeks ago by 50k • written 9.8 years ago by ▴ 40
8
votes
6
replies
449
views
DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 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 3.1 years ago by ▴ 10
4
votes
6
replies
587
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
2
votes
6
replies
391
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
24 days ago Chris • 0
3
votes
6
replies
840
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
1
vote
6
replies
1.7k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
7
votes
6
replies
448
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
1
vote
6
replies
920
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
0
votes
6
replies
773
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
6
replies
848
views
Help with model.matrix and creating the right contrast matrix for limma
limma
7 months ago • updated 4 months ago rober204 • 0
2
votes
6
replies
481
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
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
0
votes
5
replies
806
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 5 months ago by 50k • written 6 months ago by • 0
3
votes
5
replies
617
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
5
votes
5
replies
794
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
6
votes
5
replies
6.2k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
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
0
votes
5
replies
913
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
6 months ago dorota.komar • 0
1
vote
5
replies
1.0k
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 9 months ago by 50k • written 10 months ago by • 0
0
votes
5
replies
538
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.1k • written 3 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
884
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
4
votes
5
replies
870
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 7 months ago by 50k • written 7 months ago by ▴ 10
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
2
votes
4
replies
626
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
0
votes
4
replies
366
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
0
votes
4
replies
914
views
Limma multi-group, nested analysis with aggregation
limma
12 months ago • updated 9 months ago Jonathan ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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