Showing : limma • reset
5
votes
25
replies
990
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
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago Chris ▴ 10
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
28 days ago • updated 17 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
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 10 months ago by 50k • written 11 months ago by • 0
3
votes
10
replies
451
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 8 days ago by 65k • written 11 days ago by • 0
5
votes
9
replies
975
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
592
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
8
replies
564
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
540
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 25 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
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
6
votes
7
replies
795
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
7
replies
363
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 25 days ago hortense96 • 0
1
vote
7
replies
877
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
5
votes
7
replies
487
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
8
votes
6
replies
504
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
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
2
votes
6
replies
560
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
10 weeks ago • updated 7 weeks ago Lily Cheang ▴ 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
0
votes
6
replies
867
views
Help with model.matrix and creating the right contrast matrix for limma
limma
8 months ago • updated 5 months ago rober204 • 0
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
3
votes
6
replies
861
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
809
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
4
votes
6
replies
641
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
953
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
7
votes
6
replies
481
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
461
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
3
votes
5
replies
670
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
0
votes
5
replies
833
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 5 months ago by 50k • written 6 months ago by • 0
5
votes
5
replies
825
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
6
votes
5
replies
6.3k
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
891
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
968
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
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
606
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
926
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
1
vote
4
replies
661
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
394
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
1
vote
4
replies
746
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
0
votes
4
replies
950
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
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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