Showing : DEseq2 • reset
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DESeqDataSetFromTximport not found
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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1
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694
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DESeq analysis with a two-factorial design and compare the results to the unifactorial analysis
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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1
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2.4k
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Struggling with use and interpretation of "Group-specific condition effects, individuals nested within groups"
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
2
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2
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6.2k
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choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 2.1 years ago by • 0 • written 8.0 years ago by ▴ 80
7
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2
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4.2k
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Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2 ruvseq spike-in time course time series
updated 8.0 years ago by ▴ 980 • written 8.0 years ago by ▴ 20
3
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1
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1.4k
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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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4
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1.8k
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DESeq2 Different Results when using different foreach parallel backends
deseq2 biocparallel
8.0 years ago brnleehng • 0
0
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3
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2.7k
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How to compare the design formulas of DESeq2?
deseq2
8.0 years ago analeigh.gui ▴ 20
0
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1
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774
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Extreme log2 FC from DESeq2
rnaseq deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
3
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7
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3.9k
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Deseq2 - Time-series data with 2 treatments and 1 control
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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4
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3.2k
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tximport of kallisto files
tximport deseq2 kallisto
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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1
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993
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DESeq2 : how to make model contrast with multifactors : cond1(env1 versus env2) versus cond2(env1 versus env2) ?
deseq2 makecontrasts
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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5
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2.2k
views
normalization of CHIP-seq samples (ChIP and INPUT)
edgeR deseq2 voom limma
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 670
0
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7
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2.1k
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DESeq2 estimateSizeFactors controlGenes return an error
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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3
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1.6k
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Choosing DESeq2 design for mice experiment
deseq2 mouse rnaseq
8.0 years ago Emilie • 0
4
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15
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5.5k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 8.0 years ago by 43k • written 8.1 years ago by ▴ 10
1
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2
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1.8k
views
DESeq2: different number of significant genes between DESeqDataSetFromMatrix and DESeqDataSetFromHTSeqCount
deseq2 deseqdatasetfrommatrix deseqdataset
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
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5
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3.1k
views
Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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7
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7.2k
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DESeq estimateSizeFactors() is returning error "Error: all(!is.na(value)) is not TRUE"
deseq2 error R estimatesizefactors zero
updated 3.7 years ago by • 0 • written 8.2 years ago by • 0
0
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1
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568
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In DESEQ2, how was the difference in deviance between the reduced model and the full model computed when using LRT test?
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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3
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1.8k
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DESeq2 threshold-based Wald tests, before or after lfcShrink?
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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5
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1.2k
views
DESeq2: Extremely large log2 expression values with little or no read evidence
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
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1
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1.8k
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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1
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1.2k
views
DESeq2 v1.16 more than two conditions
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
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1
reply
974
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NA adjp with extremely low p value
deseq2 adjusted pvalue
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 80
0
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6
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2.1k
views
DESeq2 iterate as an alternative sizeFactor estimator
deseq2 estimatesizefactors
8.0 years ago Lauma R ▴ 10
0
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1
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1.8k
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Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 20
0
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4
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1.1k
views
DESeq2 normalization without the house keeping genes
deseq2 R
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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9
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2.0k
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SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
8.1 years ago • updated 8.0 years ago engelbrecht.stephan ▴ 10
1
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2
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1.0k
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normalization of ChIP-seq
limma edgeR deseq2
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by ▴ 670
4
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7
replies
5.5k
views
DESeq2 for survival analysis
deseq2 survival rlog transformation
8.0 years ago array chip ▴ 420
0
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3
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1.7k
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DESeq2 with categorical variables only in treatment group (not in controls)
rnaseq deseq2 categorical
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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5
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5.9k
views
DESeq2: error invalid class SummarizedExperiment object when creating DESeqDataSetFromMatrix
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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3
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1.6k
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How is the within-subject correlation modeled in time course experiments in DESeq2
deseq2 timecourse
updated 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
2
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2
replies
873
views
Normalizing an entire dataset
deseq2
updated 8.0 years ago by 21k • written 8.0 years ago by ▴ 10
2
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6
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1.8k
views
Running DESeq2 with gene-dependent binary variable such as membership in pathway?
deseq2
updated 8.0 years ago by • 0 • written 8.0 years ago by • 0
0
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1
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6.9k
views
Calling differential peaks from ATAC-seq data using DEseq2
deseq2 atac-seq
updated 8.0 years ago by ★ 5.2k • written 8.0 years ago by • 0
1
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7
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5.4k
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deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
0
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1
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1.3k
views
Running DESeq2 on top variable genes?
deseq2 variance genes
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
0
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1
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2.0k
views
DESeq2, lfcShrink, "Error in results(dds.shr, name = coefAlpha) : object 'coefAlpha' not found"
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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7
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1.9k
views
Model matrix not full rank for condition-time experiment
Model matrix not full rank deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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1
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1.8k
views
Multi Anova in DESeq2
deseq2
updated 8.0 years ago by 43k • written 8.8 years ago by • 0
0
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1
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2.4k
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Error in checkFullRank(modelMatrix) : the model matrix is not full rank, ?
deseq2 filter genefilter
updated 8.0 years ago by 43k • written 8.1 years ago by • 0
0
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4
replies
2.1k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 8.0 years ago by 43k • written 8.4 years ago by • 0
0
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3
replies
2.4k
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How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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2
replies
24k
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Determining gene expression levels with DESeq2 in a design with no condition
deseq2 tcga
8.0 years ago robles.daniela • 0
1
vote
2
replies
2.4k
views
DESeq2 for differential gene expression on GTEx dataset
rnaseq deseq2 gtex
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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4
replies
1.3k
views
Multiple differential expression analyses with DESeq2
deseq2 differential gene expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
5
votes
2
replies
2.5k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
4
votes
7
replies
2.1k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
4,840 results • Page 69 of 97
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Petr • 0
The review highlights Play Regal's commitment to fast, secure withdrawals, ensuring players receive their profits quickly and reliably. Fin…
Comment: 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
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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
Comment: upstream git branches of bioc-release
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