Showing : Limma • reset
5
votes
25
replies
829
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 22 days ago by 50k • written 4 weeks ago by ▴ 10
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
28 days ago • updated 6 days ago Chris • 0
3
votes
13
replies
1.3k
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
12
votes
12
replies
799
views
Why p value inconsistent when using different number of pathway score?
limma
updated 5 days ago by ★ 3.3k • written 6 days ago by • 0
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
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago • updated 10 months ago Anna ▴ 20
5
votes
9
replies
865
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
16 days ago • updated 8 days ago Chris • 0
0
votes
9
replies
536
views
limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 9 days ago by 50k • written 7 months ago by ▴ 10
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 11 months ago by 50k • written 17 months ago by ▴ 20
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 3 days ago by • 0 • written 7.7 years ago by ▴ 30
2
votes
8
replies
500
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 29 days ago by 50k • written 4 weeks ago by • 0
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
3
votes
8
replies
482
views
Constrast for Time Course Experiments using Limma
limma
7 weeks ago dl17032000 • 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
5
votes
7
replies
432
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
6
votes
7
replies
750
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 8 months ago by 50k • written 9 months ago by ▴ 10
1
vote
7
replies
815
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
0
votes
7
replies
256
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
9 days ago • updated 3 days ago hortense96 • 0
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
2
votes
6
replies
453
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
1
vote
6
replies
909
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
7
votes
6
replies
435
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
4
votes
6
replies
561
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
8
votes
6
replies
429
views
DGE analysis with LIMMA
limma
updated 7 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 7.4 years ago by ▴ 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 3.1 years ago by ▴ 10
2
votes
6
replies
355
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
18 days ago Chris • 0
3
votes
6
replies
833
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
761
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
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
0
votes
6
replies
836
views
Help with model.matrix and creating the right contrast matrix for limma
limma
7 months ago • updated 4 months ago rober204 • 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 24 days ago by 50k • written 9.8 years ago by ▴ 40
3
votes
5
replies
605
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
votes
5
replies
862
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
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
4
votes
5
replies
859
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
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
0
votes
5
replies
803
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 4 months ago by 50k • written 6 months ago by • 0
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
5
votes
5
replies
782
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
6
votes
5
replies
6.1k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
0
votes
5
replies
522
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 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
895
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
2
votes
4
replies
1.2k
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
4
replies
614
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
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 10 days ago by 41k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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