Showing : limma • reset
1
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2.1k
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How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
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4
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1.0k
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Pairwise comparison for DEG analysis
limma
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
4
votes
2
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3.2k
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Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
1
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1
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807
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
5
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2
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1.2k
views
PhD student
TMM limma
2.4 years ago Nisha • 0
1
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5
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1.9k
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 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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4
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1.3k
views
Pairwise differential expression using limma
limma
2.4 years ago Melissa • 0
3
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3
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2.5k
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
2.4 years ago amnahsiddiqa ▴ 10
0
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2
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854
views
Visualization of absolute values after batch effect correction
limma
updated 2.4 years ago by ▴ 360 • written 2.4 years ago by • 0
0
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1
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879
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
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11
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2.3k
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SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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2
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1.4k
views
decideTests vs topTable results
decideTests topTable limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 20
0
votes
3
replies
998
views
limma paired design
DifferentialExpression limma
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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2
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1.1k
views
RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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3
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4.9k
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Making MDS plot
plotMDS limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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3
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1.3k
views
Extract Limma Adjusted Values for Plotting
limma
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
1
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2
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976
views
Extracting fitted expression matrix from Limma
limma
2.5 years ago sarah.kelliher • 0
3
votes
11
replies
4.8k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.5 years ago • updated 2.4 years ago Anna ▴ 20
0
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2
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1.8k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
2.5 years ago pg45863 ▴ 10
5
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8
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3.0k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 23 months ago by • 0 • written 2.5 years ago by ▴ 10
0
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1
reply
967
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
0
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1
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1.2k
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma RNASeq edgeR
2.5 years ago KATHERINE CHUERE NUNES • 0
1
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2
replies
828
views
Contrast of Contrasts in Limma
limma DifferentialExpression
2.5 years ago mpitz • 0
1
vote
3
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1.5k
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 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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0
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964
views
Volcano plot
limma AffymetrixChip
2.5 years ago e.gunaut • 0
0
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4
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1.7k
views
Limma multi-group, nested analysis with aggregation
limma
2.5 years ago • updated 2.3 years ago Jonathan ▴ 10
0
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1
reply
1.1k
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
votes
3
replies
1.5k
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 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
1
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2
replies
1.7k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.6 years ago Abdul ▴ 20
2
votes
2
replies
1.2k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.6 years ago Abdul ▴ 20
0
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2
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1.7k
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
2.6 years ago • updated 2.5 years ago qiz218591 • 0
0
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2
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1.3k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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6
replies
3.0k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.3 years ago by 53k • written 5.2 years ago by ▴ 20
2
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4
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1.4k
views
limma with or without intercept gives different results
limma rnaseq
2.6 years ago Sydney • 0
0
votes
1
reply
781
views
Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
5
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2.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.6 years ago by • 0
0
votes
1
reply
916
views
Limma for Fluidigm high throughput PCR
limma Limma Fluidigm
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
1
vote
4
replies
2.7k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
2
votes
7
replies
1.7k
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 40
0
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0
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750
views
Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.7 years ago Aashil • 0
0
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0
replies
734
views
Some questions regarding using limma and interpretation
limma
2.7 years ago Sep • 0
1
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2
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1.2k
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
2.7 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 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
2
replies
1.3k
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
0
votes
2
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1.2k
views
Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
0
votes
1
reply
934
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
1
vote
3
replies
1.2k
views
Calculating the contrast of two genotypes "vs"
limma
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
0
votes
17
replies
3.0k
views
How to check linear model
modalmatrix limma R linear
2.7 years ago Jitendra ▴ 10
4,225 results • Page 5 of 85
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
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Popular Question to edward.esiribloom • 0
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