Showing : DeSeq2 • reset
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 24 months ago by 68k • written 24 months ago by • 0
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2
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872
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 3 months ago by ▴ 10 • written 24 months ago by • 0
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2
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2.4k
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DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink GSEABenchmarkeR DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
2
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2
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1.8k
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How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 24 months ago by • 0
3
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2
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1.3k
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tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
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3
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1.3k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.0 years ago Karthik • 0
0
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3
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2.7k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.0 years ago Oenone • 0
1
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1
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616
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Lower FDR cutoff gives more gene counts
DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
1
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1
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773
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
1
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1
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739
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Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
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820
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How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
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851
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DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
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2
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1.3k
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Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
2.0 years ago yee • 0
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2
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976
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Batch correction where one of the batches only has a single sample
DESeq2
2.0 years ago Tom ▴ 10
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3
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1.2k
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Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
2.0 years ago claire • 0
2
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3
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1.5k
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.0 years ago Karthik • 0
0
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1
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790
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 10
2
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2
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1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.0 years ago Manthos • 0
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4
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1.4k
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Can DESeq2 be used to compare groups of genes?
DESeq2
2.0 years ago pl23 • 0
2
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2
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1.1k
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Predicting missing values splines DESeq2
deseq DESeq2
2.0 years ago georgii.vdovin • 0
0
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1
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587
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DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
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2
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1.4k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
2.1 years ago anton.kratz ▴ 60
0
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1
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891
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.0 years ago by ★ 13k • written 2.1 years ago by • 0
4
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9
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2.1k
views
DESeq2 unable to handle large count values
DESeq2
updated 13 months ago by 43k • written 2.1 years ago by • 0
2
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5
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2.6k
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SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
reply
820
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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904
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DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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825
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
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975
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.1 years ago Ben ▴ 10
0
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9
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3.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.1 years ago by • 0 • written 8.1 years ago by ▴ 60
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2
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2.6k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
2.1 years ago RHEA • 0
1
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1
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607
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DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by ▴ 50
0
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7
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4.4k
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Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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3
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891
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DESeq2: FPMs varying based on sample groups used
DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
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8
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1.6k
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
2.1 years ago Luca • 0
0
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1
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2.6k
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Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
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10
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2.4k
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Accounting for Batch effect reduces DEGs drastically
DESeq2
2.1 years ago rohitsatyam102 ▴ 20
0
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6
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2.3k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.1 years ago erika.maldonado-rosado • 0
0
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2
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1.0k
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How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
0
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4
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1.4k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 months ago by 43k • written 2.1 years ago by • 0
2
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3
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2.7k
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
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2
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759
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DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.1 years ago Roey Angel • 0
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2
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1.1k
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.1 years ago Karthik • 0
0
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1
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1.9k
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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0
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729
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.1 years ago Florian • 0
0
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1
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2.2k
views
choosing rank for GSEA
gsea DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
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1
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1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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3
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1.3k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
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11
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2.9k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
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1.1k
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Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.1 years ago georgii.vdovin • 0
4,840 results • Page 9 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
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
Awards • All
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Popular Question to James W. MacDonald 68k
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