Showing : DEseq2 • reset
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 12 weeks ago by ▴ 10 • written 24 months ago by • 0
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 23 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 24 months ago by 68k • written 24 months ago by • 0
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 • updated 24 months ago Karthik • 0
0
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3
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2.6k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
24 months ago Oenone • 0
1
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1
reply
615
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Lower FDR cutoff gives more gene counts
DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
1
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1
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767
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
1
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1
reply
732
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Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
0
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1
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812
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How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
0
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1
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849
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DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
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 • updated 24 months ago yee • 0
0
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2
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972
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Batch correction where one of the batches only has a single sample
DESeq2
2.0 years ago • updated 24 months ago Tom ▴ 10
0
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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 • updated 24 months 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 • updated 24 months ago Karthik • 0
0
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1
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785
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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
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2
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1.1k
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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
1
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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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586
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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
0
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2
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1.4k
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DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
2.0 years ago anton.kratz ▴ 60
0
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1
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887
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.0 years ago by ★ 13k • written 2.0 years ago by • 0
4
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9
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2.1k
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DESeq2 unable to handle large count values
DESeq2
updated 13 months ago by 43k • written 2.0 years ago by • 0
2
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5
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2.5k
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
reply
817
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DESeq2 model for two genome system
RNASeq DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
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1
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898
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DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
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1
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821
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
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2
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966
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.1 years ago • updated 2.0 years ago Ben ▴ 10
0
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9
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3.2k
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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
0
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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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606
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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
views
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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885
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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
0
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8
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1.6k
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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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2.6k
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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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753
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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
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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1.8k
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DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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0
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728
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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
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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
reply
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
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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
views
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
3
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5
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1.7k
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DESeq2: Design model includes sex but only one female
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
4,839 results • Page 9 of 97
Recent ...
Replies
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Votes
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
A: p.adjust BH generates duplicate values
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