Showing : DifferentialExpression • reset
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
22 months ago Shaimaa Gamal • 0
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 22 months ago by 53k • written 23 months ago by • 0
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 23 months ago by 53k • written 23 months ago by • 0
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 23 months ago by • 0
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5
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1.4k
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Help with model for differential expression analysis
DifferentialExpression edgeR
23 months ago • updated 22 months ago Lucy ▴ 60
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3
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1.2k
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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1
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973
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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4
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1.2k
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 23 months ago by 53k • written 23 months ago by • 0
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2
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1.2k
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
24 months ago Luca • 0
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1.4k
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by ▴ 10
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4
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1.2k
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 60
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
2.1 years ago Luca • 0
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876
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.1 years ago nromerov • 0
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1.6k
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.2 years ago by 16k • written 2.2 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
2.2 years ago Shihui • 0
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1
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834
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''Model_Matrix'' error
DifferentialExpression limma
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
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3
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1.0k
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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3
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900
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.2 years ago Beyza • 0
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1
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854
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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 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
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Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
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7
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5.3k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.3 years ago by • 0 • written 4.6 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 2.3 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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6
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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1.3k
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.4 years ago Matteo • 0
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1
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965
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NA p values in edgeR results
DifferentialExpression edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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8
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3.3k
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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 2.5 years ago by ▴ 10
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limma paired design
DifferentialExpression limma
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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1
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849
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
1
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0
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1.0k
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
2
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6
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1.9k
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How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 2.5 years ago by 4.2k • written 2.5 years ago by • 0
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4
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1.4k
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.5 years ago sreeshmaraj72 • 0
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976
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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 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
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3
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1.9k
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by ▴ 20
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1.2k
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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4
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2.2k
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enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
2.6 years ago ruba-mahmoud • 0
1
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2
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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2
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1.3k
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
2.6 years ago António Miguel de Jesus Domingues ▴ 510
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2
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844
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Contrast of Contrasts in Limma
limma DifferentialExpression
2.6 years ago mpitz • 0
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3
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1.6k
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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 2.6 years ago by 53k • written 2.6 years ago by • 0
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2
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1.8k
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.6 years ago by ★ 5.0k • written 2.6 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
2.6 years ago AZ ▴ 30
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0
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758
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.7 years ago Aashil • 0
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1
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1.4k
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Analyse of MASS spectrometry proteomics data
DifferentialExpression MassSpectrometry
updated 2.7 years ago by • 0 • written 3.2 years ago by • 0
3
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6
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2.4k
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do I have to do this step in creating DGEList ?
DifferentialExpression
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
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 2.8 years ago by 53k • written 2.8 years ago by • 0
6
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11
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2.4k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.8 years ago mohammedtoufiq91 ▴ 10
201 results • Page 2 of 5
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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