Showing : DESEQ2 • reset
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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
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3
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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
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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
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2
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1.7k
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sigh of log2FC values in DESeq2
sign FoldChange DESeq2 reference
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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2
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1.8k
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Ashr and IHW
Ashr LFCShrinkage IHW DESeq2
3.9 years ago Bex • 0
2
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9
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6.2k
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Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 3.6 years ago by 43k • written 3.9 years ago by ▴ 10
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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4
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3.5k
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Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 24 months ago by 53k • written 3.9 years ago by ▴ 10
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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
3.9 years ago • updated 3.8 years ago Andrey • 0
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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 3.9 years ago by 43k • written 3.9 years ago by • 0
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1.7k
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DESeqDataSet design issue
DESeq DESeq2
3.9 years ago matthew.valentine • 0
2
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1
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1.7k
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Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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997
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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DESeq2 - batch, condition and tissue information
DESeq2
3.9 years ago Ela__77 ▴ 10
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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
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Design formula in DESeq2
groups dispersion DESeq2 desing
4.0 years ago • updated 3.9 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
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925
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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
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1
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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
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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
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2
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1.2k
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deseq2 datasetfrommatrix
DESeq2
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
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1
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1.2k
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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
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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
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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
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2.0k
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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
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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
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4
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5.1k
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Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
4.0 years ago kristoffersandas • 0
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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
4.3 years ago • updated 3.0 years ago soda ▴ 80
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2.7k
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DESeq2 - VST data
DESeq2 VST
4.0 years ago AP • 0
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1.2k
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betaPrior and lfcShrink
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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1
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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
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1
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1.1k
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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
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8
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2.3k
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Annotating DESeq2 Differential Expression Results
biomaRt DESeq2
4.0 years ago adeler001 • 0
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4
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2.3k
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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
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3
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919
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Which interactions terms to choose?
interac DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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6
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1.6k
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DESeq2 log2Foldchange issue
DESeq2
4.0 years ago Cheryl • 0
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1.1k
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Variation in number of DEGs on LFC shrinkage
DESeq2 lfcShrink
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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3
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1.1k
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Complex Contrast in DESeq2
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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2
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1.5k
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.0 years ago by ★ 1.4k • written 4.0 years ago by • 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
4.0 years ago adeler001 • 0
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1
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884
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DESeq2 Timecourse design
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
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5
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Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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1
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954
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Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
6
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10
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2.4k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 20
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1
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1.3k
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DESeq2 design formula
DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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2
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1.6k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.0 years ago m.glymenaki • 0
5
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4
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1.3k
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DESeq2 with multiple variable give me different results
Factor Levels Dispersionestimates DESeq2
4.0 years ago rafaelsolersanblas ▴ 50
4,838 results • Page 25 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/ [fnf][1] …
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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