Showing : DeSeq2 • reset
1
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5
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undefined columns selected
DESeq2
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
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2
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2.2k
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error in file(file, "rt") when reading in sample sheet using DESeqDataSetFromHTSeqCount
DESeq2
4.4 years ago Yihan • 0
1
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2
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1.0k
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Doing multiple comparisons in a DESeq2 object with multiple conditions
DESeq2
4.4 years ago jenabris • 0
3
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16
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3.8k
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DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 22 months ago by 4.2k • written 4.4 years ago by ▴ 10
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4
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2.8k
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estimateSizeFactors throws "Error in .local(object, ..., value) : all(!is.na(value)) is not TRUE". Identified root cause within estimateSizeFactorsFo…
DESeq2
4.4 years ago alawrence2211 • 0
3
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4
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4.7k
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Clarification re VST transformed data in DESeq2
DESeq2
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
0
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1
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1.4k
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DESseq2 question about VST and rlog
DESeq2 Normalization
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
2
votes
1
reply
994
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
3
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3
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1.8k
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How is DESeq2 handling replicates?
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
0
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6
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1.5k
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Bias of lowly expressed genes in DESeq2
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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2
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2.5k
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DESeq2 for longitudinal data
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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3
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949
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Highly left- skewed raw pvalues from DESeq2 analysis
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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6
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1.3k
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DESeq2 time course confusion
DESeq2 DifferentialExpression
4.4 years ago rajpal22288 ▴ 10
2
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2
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895
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dispersion increasing for extreme high mean counts
DESeq2
4.4 years ago XTR5 ▴ 10
0
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2
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1.9k
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Install older version of DESeq2 for use on cluster with older version of R
DESeq2 BiocVersion
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
1
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5
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2.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 16 months ago by ▴ 70 • written 4.5 years ago by ▴ 60
1
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1
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1.4k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
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3
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1.4k
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DESeq2: NA's in mcols(object)$betaConv
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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2
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731
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DESeq2: One or more designs for contrasts of interest
DESeq2
4.5 years ago Mirin1357 • 0
2
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2
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2.4k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.5 years ago SUMIT • 0
0
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2
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2.4k
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
4.5 years ago Clara ▴ 10
2
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6
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6.1k
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Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago reganhayward • 0
3
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5
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4.3k
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 60
0
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7
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1.5k
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matrix with Salmon gene-level quantifications in DESeq
DESeq2
4.5 years ago • updated 4.4 years ago luca.s ▴ 50
0
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8
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2.9k
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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1
reply
766
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DESeq2 - how to account for patient, batch and condition
DESeq2
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
2
votes
4
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1.8k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.3 years ago by 43k • written 4.5 years ago by • 0
0
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9
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2.6k
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Why is my plot count does not fit with log fold change result?
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
0
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4
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1.1k
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Number of genes differs between two design formulas in deseq2
DESeq2
4.5 years ago Mohamed Malek • 0
1
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6
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2.6k
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Statistics on normalized counts
DESeq2
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
0
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3
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1.9k
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[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
1
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1
reply
1.0k
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DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 10
0
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1
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729
views
Why is the number of DEG different when comparing A versus B and B versus A?
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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2
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1.4k
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where to download practice data
DESeq2
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
0
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1
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982
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DESeq2: Paired samples (before and after treatment) with different responses
DESeq2
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
2
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2
replies
909
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How to remove batch effect from multiple rna-seq dataset before running deseq2
DESeq2
4.5 years ago Yosapol • 0
0
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1
reply
1.6k
views
Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
4.5 years ago Serge • 0
0
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3
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1.4k
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
1
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1
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1.7k
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[DESeq2] - Making DESeq Dataset object from csv of already normalized counts.
DESeq2
4.5 years ago Michael • 0
0
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2
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809
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DESeq2 - Cannot replicate log2FC calculations
DESeq2
4.5 years ago Sara • 0
2
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2
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2.3k
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DESeq2 time-series with two conditions and several patients
DESeq2
4.5 years ago Karolina Trachtova ▴ 10
1
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2
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2.2k
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Design Formula, PCA, and Sex Effect
DESeq2
4.5 years ago GHI ▴ 10
0
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5
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1.8k
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
4
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3
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2.1k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 40
0
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1
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1.2k
views
FDR Correction
dada2 Metagenomics DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
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8
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3.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.5 years ago Jane ▴ 10
6
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12
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3.1k
views
ColData use only certain variable within
DESeq2
4.5 years ago Bine ▴ 50
0
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2
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2.0k
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 3.5 years ago by ▴ 10 • written 4.5 years ago by • 0
1
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2
replies
3.5k
views
Plotting FPKM
ggplots2 DESeq2 fpkm()
4.5 years ago GA ▴ 10
1
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4
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1.1k
views
Incorrect 2-fold change reported in DESeq2 Data
DESeq2
4.5 years ago Naphtap92 ▴ 10
4,840 results • Page 29 of 97
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
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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