Showing : DeSeq2 • reset
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
13 months ago Kucsera • 0
1
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1
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597
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
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9
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1.7k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 13 months ago by ▴ 40
4
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2
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1.3k
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
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5
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1.2k
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Deseq2 Design
RNASeq DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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5
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1.3k
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p value is 0, padj is 0
DESeq2
13 months ago Wirayatida • 0
1
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2
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1.3k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
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7
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1.4k
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 months ago by • 0 • written 13 months ago by • 0
0
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1
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604
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 months ago by 43k • written 13 months ago by ▴ 20
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3
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839
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DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by 68k • written 14 months ago by • 0
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4
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1.0k
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lfcShrink and alpha value
lfcShrink DESeq2
14 months ago anon • 0
2
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1
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847
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 14 months ago by 43k • written 14 months ago by • 0
0
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2
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543
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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2
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544
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
14 months ago Anna • 0
1
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2
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857
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Deseq2 res Function
DESeq2
updated 14 months ago by 68k • written 14 months ago by ▴ 10
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4
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818
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
14 months ago NB • 0
0
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5
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816
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Identical samples after deseq2 batch effect removal
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
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632
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
1
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2
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539
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
14 months ago Denise • 0
0
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1
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474
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eRNAs count
RNASeq DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
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667
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DESeq2 rerun returns different results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
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574
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
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711
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
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2
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1.2k
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Handling biological replicates in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 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 7.1 years ago by ▴ 30
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6
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1.7k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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2
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602
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 15 months ago by • 0
4
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5
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1.5k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
15 months ago LuciaNhu • 0
0
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1
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817
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Average expression of genes across replicates
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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0
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470
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
15 months ago info ▴ 10
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11
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2.7k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 10 months ago by • 0 • written 15 months ago by • 0
0
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1
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587
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Deseq to output continous sequencing data
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
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4
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1.5k
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Adjusted p-values become NA when sub-setting samples
DESeq2
15 months ago • updated 14 months ago txema.heredia • 0
3
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3
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1.7k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 15 months ago by • 0
0
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2
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1.0k
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 15 months ago by • 0
0
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1
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518
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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3
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1.4k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
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4
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1.2k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
15 months ago boczniak767 ▴ 740
0
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1
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413
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
15 months ago JY • 0
0
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1
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503
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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2
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541
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how to extract expression matrix post deseq2
DESeq2
written 15 months ago by • 0
0
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2
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576
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Using Normalized Counts in DESeq2
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
3
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2
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688
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When running contrasts, does it use normalized read counts?
DESeq2
15 months ago Katherine ▴ 20
0
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1
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451
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
3
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4
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1.5k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
15 months ago Eva ▴ 10
1
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4
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1.5k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 15 months ago by ★ 5.0k • written 16 months ago by • 0
0
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1
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565
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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4
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1.1k
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 15 months ago by • 0
5
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4
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1.1k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 16 months ago by • 0
4,848 results • Page 3 of 97
Recent ...
Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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