Showing : DifferentialExpression • reset
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.8 years ago • updated 2.7 years ago dqt • 0
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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 2.8 years ago by 53k • written 2.8 years ago by • 0
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Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
2.8 years ago Jayesh Kumar • 0
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 2.9 years ago by • 0
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
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How to interpret MAST coefficients
DifferentialExpression MAST
updated 4 months ago by ▴ 10 • written 3.0 years ago by • 0
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How to subset a list of genes from a curated reference list of genes
R subset DifferentialExpression
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
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Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 2.9 years ago by 68k • written 3.0 years ago by • 0
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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 3.0 years ago by 68k • written 3.0 years ago by • 0
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adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.0 years ago Kevin Gregory ▴ 10
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weighting sample group
monocle SingleCell DifferentialExpression
3.1 years ago Sogand • 0
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DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
3.1 years ago António Miguel de Jesus Domingues ▴ 510
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Swish log2FC NA output
swish fishpond DifferentialExpression
3.2 years ago jvandinter • 0
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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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 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
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Error while running DESeq2
DifferentialExpression
3.3 years ago srikar • 0
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.3 years ago Nik Tuzov ▴ 90
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.3 years ago giBio • 0
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1.0k
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Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.4 years ago by • 0
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4
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1.5k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
3.3 years ago S • 0
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1.0k
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.4 years ago by ▴ 10
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1.5k
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How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
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Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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1.6k
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edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.4 years ago Sarah • 0
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3.0k
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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
3.5 years ago Ismail • 0
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1.9k
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Which Limma guide is recommended ?
limma R DifferentialExpression
3.5 years ago • updated 3.4 years ago JAcky • 0
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How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
3.5 years ago mohammedtoufiq91 ▴ 10
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Getting erros from dds
DifferentialExpression DESeq2
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
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2.0k
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DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 20 months ago by ★ 5.0k • written 3.6 years ago by ▴ 70
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3.9k
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
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1.7k
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Complex contrasts in limma
RNASeq limma DifferentialExpression
3.6 years ago tcalvo ▴ 100
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.6 years ago nhaus ▴ 70
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2.0k
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How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by ▴ 70
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What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.4 years ago by • 0 • written 3.6 years ago by ▴ 70
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2
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2.6k
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
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672
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Error in DEqMS proteomics analysis
DEqMS R DifferentialExpression
3.7 years ago Mrinal.singh06 • 0
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3
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1.7k
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Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
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2
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1.3k
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.7 years ago IamFrofro • 0
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5
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2.4k
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Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
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3
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2.4k
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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8
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.8 years ago • updated 3.7 years ago dadca596 • 0
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883
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NanoStringDiff
DifferentialExpression NanoStringDiff
3.8 years ago sanrie10 • 0
198 results • Page 3 of 4
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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