Showing : DEseq2 • reset
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Gene ID Duplicates
deseq2 genetics Tutorial
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
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3
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6.8k
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How are the shrunk result data used in DESeq2?
deseq2 lfcshrink
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
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4
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1.7k
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Inconsistent RNAseq data in knockdown expt
deseq2
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by • 0
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2
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1.3k
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Likeliness Ratio Test
deseq2 design and contrast matrix
7.7 years ago csijst • 0
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13
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2.5k
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contrast design of DESeq2 for correlated data
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
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Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
7.7 years ago blehtine • 0
4
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3
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Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2 tximport org.mm.eg.db gencode
7.7 years ago pvd2107 ▴ 30
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1.8k
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How to correctly set DESeq2 design
deseq2
7.7 years ago Lauma R ▴ 10
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1
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2.0k
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Error while Installing DESeq2
software error R deseq2 rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
2
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3
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1.0k
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Question concerning the testing of interactions using the group design and the use of lfcShrink() (DESeq2)
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 40
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5
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1.7k
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Deviance decomposition with DESeq2
deseq2 analysis of deviance
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
3
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3
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7.7k
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Interpreting results of DESeq2, regarding baseMean and log2FoldChange.
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
0
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1
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1.7k
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DESeq2: gene-wise dispersion estimates stuck on running
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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2
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871
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In DE experiment with multiple contrasts, is it possible to merge only relevant counts column back to the results, versus all (by default) counts col…
deseq2
7.7 years ago JP Cartailler ▴ 40
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DESeq2: How to get sizeFactor per library when importing counts with tximport?
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 270
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4
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866
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Problem in designing result in DESeq2
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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1
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699
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Time-series Experiments with Varied Drug Concentrations Design Matri
deseq2 rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
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1
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1.4k
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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1.1k
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DESeq2 Error: Error in if (assays_nrow != rowData_nrow) { : argument is of length zero
deseq2
7.7 years ago 929072397 • 0
0
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3
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1.8k
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Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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14
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6.2k
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DESeq2 count normalization
deseq2 normalization normalized counts
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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8
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1.6k
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DESeq2 one group vs multigroup comparison error
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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8
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15k
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DESeq2: one condition vs multiple combined
rnaseq deseq2
updated 7.7 years ago by ▴ 10 • written 9.3 years ago by ▴ 40
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1
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1.0k
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Meaning of the intercept when betaPrior is TRUE?
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 60
2
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4
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1.9k
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Unmix() function in DeSeq capabilities
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 170
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2.7k
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DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
7.7 years ago SPbeginner • 0
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[DESeq2] Results summary indicates LFC > and < 0 even with changed lfcThreshold
DESeq2 lfcThreshold
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
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739
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processing deseq2 result
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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3
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4.6k
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Error when constructing DESeqDataSetFromMatrix (Error in round(assay(se)): non-numeric argument to mathematical function)
deseq2 R error
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
5
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14
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9.0k
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DESeq2 vs Ballgown results
ballgown deseq2
7.7 years ago CE ▴ 20
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3.2k
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[DESeq2] Odd patterns in MA plot
deseq2 MA-plot
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
0
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5
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1.7k
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differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ★ 1.5k
6
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4
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2.1k
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
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5
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2.5k
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DESeq LRT test and construction of Co-expression network
LRT co-expression network deseq2 time course experiment network analysis
updated 2.5 years ago by • 0 • written 7.7 years ago by ▴ 30
5
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3
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18k
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Interpreting heatmap in DESEQ2
deseq2 heatmap.2
updated 7.7 years ago by ▴ 170 • written 7.7 years ago by • 0
2
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6
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2.7k
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Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
7.7 years ago casey.rimland ▴ 170
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3
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1.1k
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DESeq2- Another Multi-factor Question
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
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2
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794
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DESeq2 - Effect of DDS Import of All vs Select Conditions
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 30
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5
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27k
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package DESeq2 installation with R.
deseq2 R package installation
updated 4.5 years ago by 43k • written 7.7 years ago by • 0
3
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3
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1.8k
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Difficulties with probable batch effect in paired blocked (treatment and placebo) experiment
deseq2 edger limma batch effect paired design
7.7 years ago Vladimir Krasikov ▴ 90
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2
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3.2k
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how can I interpret the fold change of Dseq2
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 30
1
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3
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3.7k
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duplicated row names when creating DESeqDataSetFromMatrix
deseq2 DESeqDataSetFromMatrix duplicate
updated 7.7 years ago by 68k • written 7.7 years ago by ★ 1.5k
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2
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1.8k
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Is there a data package containing complex RNA-Seq data?
RNAseqdataset airway deseq2 rangedsummarizedexperiment rnaseqgene
updated 7.7 years ago by ▴ 160 • written 7.7 years ago by • 0
1
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4
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3.2k
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If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
7
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10
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7.7k
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Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 7.7 years ago by ▴ 30 • written 9.3 years ago by ▴ 50
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1
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1.2k
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tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
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4
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1.3k
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Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
7.7 years ago jaime.alvarez.benayas • 0
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5
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1.4k
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DESeq2: normalization of experiments sequenced separately
RNAseq normalization deseq2
7.7 years ago uguy • 0
1
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4
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1.3k
views
How to handle strong batch effects
deseq2
7.7 years ago jovel_juan ▴ 30
0
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4
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1.1k
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DESeq2 Control for differences between patients
deseq2
updated 7.7 years ago by ★ 1.4k • written 7.7 years ago by ▴ 10
4,840 results • Page 65 of 97
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Replies
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
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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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