Showing : Limma • reset
1
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2
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1.7k
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loading scores using plotMDS in limma
plotMDS limma
2.5 years ago Cen • 0
2
votes
1
reply
1.2k
views
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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1.3k
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Fluidigm Data Batch Correction
sva limma
updated 2.5 years ago by 53k • written 2.6 years ago by • 0
0
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2
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1.2k
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.5 years ago Eleonora • 0
3
votes
2
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821
views
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
reply
2.3k
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How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 2.6 years ago by 53k • written 2.6 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 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
4
votes
2
replies
3.9k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
1
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1
reply
866
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
5
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2
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1.3k
views
PhD student
TMM limma
2.6 years ago Nisha • 0
1
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5
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2.1k
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 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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4
replies
1.4k
views
Pairwise differential expression using limma
limma
2.6 years ago Melissa • 0
3
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3
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2.8k
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
2.6 years ago amnahsiddiqa ▴ 10
0
votes
2
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890
views
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
reply
936
views
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
votes
11
replies
2.5k
views
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
replies
1.5k
views
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
replies
1.1k
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
replies
1.1k
views
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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5.2k
views
Making MDS plot
plotMDS limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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3
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1.4k
views
Extract Limma Adjusted Values for Plotting
limma
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
3
votes
6
replies
1.7k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
1
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2
replies
1.1k
views
Extracting fitted expression matrix from Limma
limma
2.7 years ago sarah.kelliher • 0
3
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11
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5.3k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.7 years ago Anna ▴ 20
0
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2
replies
1.9k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
2.7 years ago pg45863 ▴ 10
5
votes
8
replies
3.2k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 2.2 years ago by • 0 • written 2.7 years ago by ▴ 10
0
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1
reply
1.0k
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
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1
reply
1.2k
views
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
replies
1.2k
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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872
views
Contrast of Contrasts in Limma
limma DifferentialExpression
2.7 years ago mpitz • 0
1
vote
3
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1.7k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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0
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1.0k
views
Volcano plot
limma AffymetrixChip
2.8 years ago e.gunaut • 0
0
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4
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1.8k
views
Limma multi-group, nested analysis with aggregation
limma
2.8 years ago • updated 2.5 years ago Jonathan ▴ 10
0
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1
reply
1.2k
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
2
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3
replies
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 2.8 years ago by 68k • written 2.8 years ago by ▴ 10
1
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2
replies
1.9k
views
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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1.9k
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
2.8 years ago qiz218591 • 0
0
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2
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1.4k
views
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
replies
3.2k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.5 years ago by 53k • written 5.4 years ago by ▴ 20
2
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4
replies
1.6k
views
limma with or without intercept gives different results
limma rnaseq
2.9 years ago Sydney • 0
0
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1
reply
829
views
Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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5
replies
2.4k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.9 years ago by • 0
0
votes
1
reply
969
views
Limma for Fluidigm high throughput PCR
limma Limma Fluidigm
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
1
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4
replies
2.8k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
2
votes
7
replies
1.8k
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 40
0
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0
replies
789
views
Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.9 years ago Aashil • 0
0
votes
0
replies
759
views
Some questions regarding using limma and interpretation
limma
2.9 years ago Sep • 0
1
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2
replies
1.3k
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.9 years ago Yang Shi ▴ 10
4,230 results • Page 5 of 85
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Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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