Showing : DifferentialExpression • reset
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 21 months ago by 53k • written 21 months ago by • 0
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 21 months ago by • 0
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5
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Help with model for differential expression analysis
DifferentialExpression edgeR
21 months ago • updated 20 months ago Lucy ▴ 60
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3
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981
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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4
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 21 months ago by 53k • written 22 months ago by • 0
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2
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1.1k
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
22 months ago Luca • 0
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2
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
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743
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 22 months ago by 43k • written 23 months ago by ▴ 10
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4
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1.1k
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 23 months ago by 43k • written 23 months ago by ▴ 60
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
23 months ago Luca • 0
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845
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
24 months ago nromerov • 0
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6
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1.5k
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
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4
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.0 years ago Shihui • 0
0
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1
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806
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''Model_Matrix'' error
DifferentialExpression limma
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
3
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3
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951
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.0 years ago by 68k • written 2.1 years ago by • 0
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3
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861
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
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2
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1.0k
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.1 years ago Beyza • 0
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1
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811
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
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1
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787
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Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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7
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5.2k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.1 years ago by • 0 • written 4.5 years ago by ▴ 20
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3
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1.2k
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DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
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0
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766
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DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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6
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1.4k
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
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2
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1.2k
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.2 years ago Matteo • 0
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1
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933
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NA p values in edgeR results
DifferentialExpression edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
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8
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3.2k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 2.3 years ago by ▴ 10
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3
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973
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limma paired design
DifferentialExpression limma
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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809
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
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0
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983
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.3 years ago by 43k • written 2.4 years ago by ▴ 20
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6
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1.8k
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How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 2.3 years ago by 4.2k • written 2.4 years ago by • 0
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4
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1.3k
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.4 years ago sreeshmaraj72 • 0
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931
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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 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
3
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3
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1.8k
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by ▴ 20
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1
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1.1k
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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4
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2.1k
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enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
2.4 years ago ruba-mahmoud • 0
1
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2
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1.0k
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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2
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1.2k
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
2.4 years ago António Miguel de Jesus Domingues ▴ 510
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2
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810
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Contrast of Contrasts in Limma
limma DifferentialExpression
2.4 years ago mpitz • 0
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3
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1.5k
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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 2.4 years ago by 53k • written 2.4 years ago by • 0
2
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2
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1.7k
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 30
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2
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1.5k
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.5 years ago AZ ▴ 30
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0
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732
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.6 years ago Aashil • 0
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1
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1.3k
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Analyse of MASS spectrometry proteomics data
DifferentialExpression MassSpectrometry
updated 2.6 years ago by • 0 • written 3.1 years ago by • 0
3
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6
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2.3k
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do I have to do this step in creating DGEList ?
DifferentialExpression
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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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
6
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11
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2.3k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago • updated 2.6 years ago mohammedtoufiq91 ▴ 10
6
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2
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4.1k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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1
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1.1k
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limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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4
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1.3k
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Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
198 results • Page 2 of 4
Recent ...
Replies
Comment: JunctionSeq producing strangely large effect sizes for certain exon counting bin by 97shandie • 0
That's a tricky issue! I've definitely seen similar behavior in differential exon usage analysis. It sounds like the normalization method J…
Comment: Heat Map by 97shandie • 0
Hi Dania, it looks like you're on the right track building your heatmap! It's great you've already filtered your data based on adjusted p-v…
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Results with PON give more variants by ejafgdf4.ge.r.m • 0
It s common to expect Mutect2 with a PON to be a strict subset of Mutect2 without it but seeing unique variants in Mutect2withPON isn t unu…
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…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Comment: 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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