Showing : DeSeq2 • reset
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DESeq2: model matrix is not full rank
DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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0
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836
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
3.9 years ago Jonas • 0
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2
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1.5k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.9 years ago by ★ 13k • written 3.9 years ago by • 0
0
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3
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1.7k
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Is it possible to specify random nested factor in DEseq2?
nested DESeq2
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
2
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2
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5.1k
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EdgeR installation issue
limma edgeR DESeq2
3.9 years ago aonghus • 0
0
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2
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1.7k
views
sigh of log2FC values in DESeq2
sign FoldChange DESeq2 reference
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
3
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2
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1.8k
views
Ashr and IHW
Ashr LFCShrinkage IHW DESeq2
4.0 years ago • updated 3.9 years ago Bex • 0
2
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9
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6.2k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 3.6 years ago by 43k • written 4.0 years ago by ▴ 10
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2
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1.3k
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
4
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4
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3.5k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 2.0 years ago by 53k • written 4.0 years ago by ▴ 10
3
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2
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1.1k
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P-values change 100-fold with only a single count changed
DESeq2
4.0 years ago • updated 3.9 years ago Andrey • 0
0
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1
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1.3k
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Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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2
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1.8k
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DESeqDataSet design issue
DESeq DESeq2
4.0 years ago matthew.valentine • 0
2
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1
reply
1.7k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
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1.0k
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
3
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3
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2.6k
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DESeq2 - batch, condition and tissue information
DESeq2
4.0 years ago Ela__77 ▴ 10
0
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9
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2.6k
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DESeq2 analyze MeRIP-seq
DESeq2 MeRIP-seq
updated 3.1 years ago by 43k • written 4.0 years ago by • 0
1
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2
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2.0k
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Design formula in DESeq2
groups dispersion DESeq2 desing
4.0 years ago m.glymenaki • 0
3
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4
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1.4k
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DESEQ2 Results log2fold and pvalue changes after removing genes
DESeq2
4.0 years ago Bine ▴ 50
0
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1
reply
930
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different results between DESeq model with multiple groups or with specific groups
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
reply
1.2k
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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3
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3.1k
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Error in DESeq2
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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2
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1.2k
views
deseq2 datasetfrommatrix
DESeq2
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
1
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1
reply
1.2k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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9
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2.5k
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DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
4.0 years ago michael.morash • 0
3
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5
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5.7k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
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1
reply
2.0k
views
values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
2
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2
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1.1k
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padjust after running DESEQ2
DESeq2
4.0 years ago Bine ▴ 50
0
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4
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5.2k
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Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
4.0 years ago kristoffersandas • 0
0
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4
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1.8k
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normalizing EXOM-seq read using DESeq2
ExomeSeq DESeq2
4.0 years ago adR ▴ 40
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2
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1.2k
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Troubleshooting DESeq2 Analysis: no DE genes found in subset
DESeq2
updated 4.0 years ago by ★ 1.4k • written 4.0 years ago by • 0
10
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23
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16k
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Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
4.4 years ago • updated 3.1 years ago soda ▴ 80
1
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4
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2.7k
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DESeq2 - VST data
DESeq2 VST
4.0 years ago AP • 0
1
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1
reply
1.2k
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betaPrior and lfcShrink
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
reply
1.6k
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Calculating gene expression dominance coefficient via DESeq2
RNASeq DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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1
reply
1.2k
views
DESeq2: Difference between two groups of conditions
factor DESeq2 MultipleComparison
updated 4.0 years ago by ★ 1.4k • written 4.0 years ago by • 0
0
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8
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2.3k
views
Annotating DESeq2 Differential Expression Results
biomaRt DESeq2
4.0 years ago adeler001 • 0
6
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4
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2.3k
views
Which rlog should I use for DESeq2 analysis
samples rlog DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 50
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5
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2.0k
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95% confidence intervals for PCA in DESEQ2
DESEQ2 DESeq2
4.0 years ago tylerdodgeball2019 • 0
0
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3
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929
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Which interactions terms to choose?
interac DESeq2
updated 4.0 years ago by 43k • written 4.1 years ago by • 0
0
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6
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1.7k
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DESeq2 log2Foldchange issue
DESeq2
4.1 years ago • updated 4.0 years ago Cheryl • 0
0
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1
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1.1k
views
Variation in number of DEGs on LFC shrinkage
DESeq2 lfcShrink
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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3
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1.1k
views
Complex Contrast in DESeq2
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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2
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1.5k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by • 0
0
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5
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1.7k
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Is there a way to get the confidence interval for the fold change generated on DESeq2
DESeq2
4.1 years ago adeler001 • 0
0
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1
reply
890
views
DESeq2 Timecourse design
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
3
votes
5
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2.5k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
reply
967
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
6
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10
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2.4k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 20
0
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1
reply
1.3k
views
DESeq2 design formula
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
4,840 results • Page 25 of 97
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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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