Showing : DeSeq2 • reset
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 11 months ago by 43k • written 11 months ago by ▴ 20
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3
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744
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DESeq2 - Comparing Comparisons
DESeq2
updated 11 months ago by 68k • written 12 months ago by • 0
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4
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930
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lfcShrink and alpha value
lfcShrink DESeq2
12 months ago anon • 0
2
votes
1
reply
712
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 12 months ago by 43k • written 12 months ago by • 0
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2
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497
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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2
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474
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
12 months ago Anna • 0
1
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2
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799
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Deseq2 res Function
DESeq2
updated 12 months ago by 68k • written 12 months ago by ▴ 10
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4
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748
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
12 months ago NB • 0
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5
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764
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Identical samples after deseq2 batch effect removal
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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1
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574
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 12 months ago by 68k • written 12 months ago by • 0
1
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2
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492
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
12 months ago Denise • 0
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1
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421
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eRNAs count
RNASeq DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
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1
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624
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DESeq2 rerun returns different results
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
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1
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527
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 12 months ago by 43k • written 12 months ago by • 0
0
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1
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594
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
2
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2
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1.1k
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Handling biological replicates in DESeq2
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.9 years ago by ▴ 30
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6
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1.6k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 months ago by 43k • written 12 months ago by ▴ 10
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2
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577
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 13 months ago by • 0
4
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5
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1.3k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
13 months ago LuciaNhu • 0
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1
reply
740
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Average expression of genes across replicates
DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
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0
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414
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
13 months ago info ▴ 10
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11
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2.5k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 8 months ago by • 0 • written 13 months ago by • 0
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1
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561
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Deseq to output continous sequencing data
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
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4
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1.4k
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Adjusted p-values become NA when sub-setting samples
DESeq2
13 months ago • updated 12 months ago txema.heredia • 0
3
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3
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1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 13 months ago by • 0
0
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2
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790
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 13 months ago by • 0
0
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1
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492
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
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4
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1.1k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
13 months ago boczniak767 ▴ 740
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1
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375
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
13 months ago JY • 0
0
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1
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472
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
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2
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493
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how to extract expression matrix post deseq2
DESeq2
written 13 months ago by • 0
0
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2
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546
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Using Normalized Counts in DESeq2
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
3
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2
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596
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When running contrasts, does it use normalized read counts?
DESeq2
13 months ago Katherine ▴ 20
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1
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423
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
3
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4
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1.3k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
13 months ago Eva ▴ 10
1
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4
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1.3k
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
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526
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
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4
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902
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 13 months ago by • 0
5
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4
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1.0k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
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2
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692
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
14 months ago paul.meraner • 0
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0
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600
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
14 months ago • updated 13 months ago info ▴ 10
1
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6
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1.5k
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heatmap with batch effect
DESeq2 BatchEffect
written 14 months ago by • 0
0
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2
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755
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
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1
reply
1.0k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
1
reply
693
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
1
reply
596
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
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2
replies
889
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
4,840 results • Page 3 of 97
Recent ...
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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