Showing : LIMMA • reset
2
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1.2k
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Grouping DEGs yields varying results
RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
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6
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1.5k
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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2
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1.2k
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Fluidigm Data Batch Correction
sva limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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2
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1.2k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.5 years ago Eleonora • 0
3
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2
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805
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For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
1
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1
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2.2k
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How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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4
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1.1k
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Pairwise comparison for DEG analysis
limma
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
4
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2
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3.6k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
1
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1
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847
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
5
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2
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1.3k
views
PhD student
TMM limma
2.5 years ago Nisha • 0
1
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5
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2.0k
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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 2.5 years ago by 53k • written 2.5 years ago by • 0
1
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4
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1.4k
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Pairwise differential expression using limma
limma
2.5 years ago Melissa • 0
3
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3
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2.7k
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
2.5 years ago amnahsiddiqa ▴ 10
0
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2
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877
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Visualization of absolute values after batch effect correction
limma
updated 2.6 years ago by ▴ 360 • written 2.6 years ago by • 0
0
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1
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918
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How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
3
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11
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2.4k
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SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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2
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1.5k
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decideTests vs topTable results
decideTests topTable limma
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 20
0
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3
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1.0k
views
limma paired design
DifferentialExpression limma
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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2
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1.1k
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RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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3
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5.1k
views
Making MDS plot
plotMDS limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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3
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1.4k
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Extract Limma Adjusted Values for Plotting
limma
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
3
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6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
1
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2
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1.0k
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Extracting fitted expression matrix from Limma
limma
2.6 years ago sarah.kelliher • 0
3
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11
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5.1k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.6 years ago Anna ▴ 20
0
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2
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1.8k
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
2.6 years ago pg45863 ▴ 10
5
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8
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3.2k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 2.1 years ago by • 0 • written 2.6 years ago by ▴ 10
0
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1
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1.0k
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
0
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1
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1.2k
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
3
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4
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1.1k
views
Anova table edgeR limma
limma RNASeq edgeR
2.7 years ago KATHERINE CHUERE NUNES • 0
1
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2
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866
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Contrast of Contrasts in Limma
limma DifferentialExpression
2.7 years ago mpitz • 0
1
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3
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1.6k
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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0
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1.0k
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Volcano plot
limma AffymetrixChip
2.7 years ago e.gunaut • 0
0
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4
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1.8k
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Limma multi-group, nested analysis with aggregation
limma
2.7 years ago • updated 2.5 years ago Jonathan ▴ 10
0
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1
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1.2k
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Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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3
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1.6k
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 2.7 years ago by 68k • written 2.8 years ago by ▴ 10
1
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2
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1.8k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.8 years ago Abdul ▴ 20
2
votes
2
replies
1.3k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.8 years ago Abdul ▴ 20
0
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2
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1.8k
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
2.8 years ago • updated 2.7 years ago qiz218591 • 0
0
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2
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1.4k
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
1
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6
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3.2k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.4 years ago by 53k • written 5.3 years ago by ▴ 20
2
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4
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1.5k
views
limma with or without intercept gives different results
limma rnaseq
2.8 years ago Sydney • 0
0
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1
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811
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Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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5
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2.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.8 years ago by • 0
0
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1
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955
views
Limma for Fluidigm high throughput PCR
limma Limma Fluidigm
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
1
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4
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2.8k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
2
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7
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1.8k
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 40
0
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0
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779
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.8 years ago Aashil • 0
0
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0
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753
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Some questions regarding using limma and interpretation
limma
2.8 years ago Sep • 0
1
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2
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1.2k
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Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.8 years ago Yang Shi ▴ 10
0
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1
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1.1k
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
4,229 results • Page 5 of 85
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Commentator to James W. MacDonald 68k
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Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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