Showing : DifferentialExpression • reset
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
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3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
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6
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792
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
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1.2k
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Which Limma guide is recommended ?
limma R DifferentialExpression
2.1 years ago • updated 2.0 years ago JAcky • 0
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449
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.0 years ago by ▴ 10
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13
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.2 years ago by ▴ 30
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
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2
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299
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago Jane ▴ 10
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11
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1.4k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
15 months ago mohammedtoufiq91 ▴ 10
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10
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1.4k
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.6 years ago • updated 3.5 years ago Hajar • 0
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3
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435
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
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3
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935
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.2 years ago nhaus ▴ 30
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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 11 months ago by • 0
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6
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1.4k
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 18 months ago by • 0
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5
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4.8k
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How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.7 years ago zhxiaokang ▴ 20
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3
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1.6k
views
differential gene expression
limma differentialexpression
updated 9.6 years ago by ▴ 760 • written 9.6 years ago by ▴ 20
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
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3
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2.9k
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Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
9.6 years ago asaferali • 0
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1
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1.6k
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.1 years ago by ▴ 10 • written 10.1 years ago by 50k
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3
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1.4k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
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7
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2.4k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 20
3
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7
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1.4k
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Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
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1
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678
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Wald or LR Test
DESeq2 DifferentialExpression
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
0
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2
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1.2k
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Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 30
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2
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2.3k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 years ago by ▴ 10
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3
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869
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 42k • written 16 months ago by • 0
5
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3
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729
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
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1
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656
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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 16 months ago by 50k • written 16 months ago by • 0
1
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2
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670
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DESeq2 with very large feature set
DESeq2 DifferentialExpression
3.5 years ago ramiro.barrantes ▴ 10
4
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2
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6.7k
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DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 9.6 years ago by 42k • written 9.6 years ago by ▴ 90
1
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2
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654
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 12 months ago by 50k • written 12 months ago by • 0
0
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3
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1.4k
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Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 3.5 years ago by 50k • written 3.5 years ago by • 0
1
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1
reply
603
views
Analysis design for DESeq2
DifferentialExpression DESeq2
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
1
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8
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1.6k
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
23 months ago giBio • 0
1
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2
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867
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
13 months ago AZ ▴ 30
2
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1
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230
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by ▴ 20
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369
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
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3
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74
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 hours ago by 42k • written 1 day ago by • 0
0
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1
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563
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
3
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6
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1.3k
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do I have to do this step in creating DGEList ?
DifferentialExpression
updated 14 months ago by 50k • written 14 months ago by • 0
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1.5k
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Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago AZ ▴ 30
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2
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1.8k
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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
2.1 years ago Ismail • 0
5
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6
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1.6k
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.3 years ago by • 0
1
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3
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932
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
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5
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1.3k
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 20 months ago by 42k • written 2.7 years ago by • 0
4
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3
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1.2k
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Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
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1
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125
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
50 results • Page 1 of 1
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Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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