Showing : DifferentialExpression • reset
6
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11
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
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2
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 10
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1
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1.3k
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limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
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4
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1.4k
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Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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1
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907
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
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2
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1.9k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
3.1 years ago dqt • 0
0
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1
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1.1k
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Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
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3
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11k
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Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
3.1 years ago Jayesh Kumar • 0
0
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3
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1.5k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.7k
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
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3
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1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
3
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6
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2.2k
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.2 years ago by • 0
3
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7
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3.0k
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
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1
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2.5k
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How to interpret MAST coefficients
DifferentialExpression MAST
updated 8 months ago by ▴ 10 • written 3.3 years ago by • 0
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1
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1.5k
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How to subset a list of genes from a curated reference list of genes
R subset DifferentialExpression
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
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7
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2.2k
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Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 3.2 years ago by 68k • written 3.3 years ago by • 0
0
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1
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2.1k
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Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
1
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0
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1.5k
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.4 years ago Kevin Gregory ▴ 10
0
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0
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942
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weighting sample group
monocle SingleCell DifferentialExpression
3.4 years ago Sogand • 0
0
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1
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872
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DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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0
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1.2k
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
3.5 years ago António Miguel de Jesus Domingues ▴ 510
0
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8
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2.2k
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Swish log2FC NA output
swish fishpond DifferentialExpression
3.5 years ago jvandinter • 0
1
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3
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1.6k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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2
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1.5k
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
1
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6
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2.0k
views
Error while running DESeq2
DifferentialExpression
3.6 years ago srikar • 0
0
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0
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1.2k
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.6 years ago Nik Tuzov ▴ 90
1
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8
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2.4k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.6 years ago giBio • 0
0
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1
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1.1k
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression DiffBind
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
0
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4
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1.6k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
3.7 years ago S • 0
0
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1
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1.1k
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
3
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8
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5.6k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.8 years ago by ▴ 10
1
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4
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1.6k
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How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
1
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1
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1.4k
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Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.7 years ago by ★ 5.0k • written 3.7 years ago by • 0
1
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2
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1.8k
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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2
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1.8k
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edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.8 years ago Sarah • 0
1
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2
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3.2k
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.8 years ago Ismail • 0
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7
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2.1k
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Which Limma guide is recommended ?
limma R DifferentialExpression
3.8 years ago JAcky • 0
3
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4
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2.1k
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How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
3.8 years ago mohammedtoufiq91 ▴ 10
0
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1
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1.2k
views
Getting erros from dds
DifferentialExpression DESeq2
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
0
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7
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2.2k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
12
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13
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14k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 2.0 years ago by ★ 5.0k • written 3.9 years ago by ▴ 70
1
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1
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4.3k
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
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2
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1.9k
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Complex contrasts in limma
RNASeq limma DifferentialExpression
3.9 years ago tcalvo ▴ 100
3
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3
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1.7k
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.9 years ago nhaus ▴ 70
1
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1
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2.2k
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How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 70
4
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5
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2.5k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.8 years ago by • 0 • written 4.0 years ago by ▴ 70
0
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2
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2.7k
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
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0
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740
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Error in DEqMS proteomics analysis
DEqMS R DifferentialExpression
4.0 years ago Mrinal.singh06 • 0
4
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3
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1.8k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
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2
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1.5k
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
4.0 years ago IamFrofro • 0
202 results • Page 3 of 5
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Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
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/
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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