Showing : DEseq2 • reset
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 1 day ago by 43k • written 10 days ago by • 0
1
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8
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577
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
updated 2 days ago by 52k • written 3 days ago by ▴ 30
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2
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226
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 days ago by ★ 4.6k • written 9 days ago by • 0
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5
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429
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Deseq2 Design
RNASeq DESeq2
updated 4 days ago by 67k • written 8 days ago by • 0
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5
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382
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p value is 0, padj is 0
DESeq2
9 days ago • updated 8 days ago Wirayatida • 0
1
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2
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402
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
10 days ago • updated 9 days ago georgii.vdovin • 0
0
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7
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670
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 days ago by • 0 • written 12 days ago by • 0
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1
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231
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 14 days ago by 43k • written 14 days ago by ▴ 20
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3
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329
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DESeq2 - Comparing Comparisons
DESeq2
updated 9 days ago by 67k • written 16 days ago by • 0
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4
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456
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lfcShrink and alpha value
lfcShrink DESeq2
22 days ago • updated 16 days ago cropero • 0
1
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1
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229
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 18 days ago by 43k • written 25 days ago by • 0
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2
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159
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 18 days ago by 43k • written 19 days ago by • 0
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2
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229
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
24 days ago • updated 23 days ago Anna • 0
1
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2
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507
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Deseq2 res Function
DESeq2
updated 26 days ago by 67k • written 28 days ago by ▴ 10
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4
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382
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
28 days ago NB • 0
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5
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379
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Identical samples after deseq2 batch effect removal
DESeq2
updated 29 days ago by 43k • written 4 weeks ago by • 0
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1
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217
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 29 days ago by 67k • written 4 weeks ago by • 0
1
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2
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279
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
4 weeks ago Denise • 0
0
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1
reply
138
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eRNAs count
RNASeq DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
0
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1
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387
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DESeq2 rerun returns different results
DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
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1
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225
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
0
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1
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191
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
2
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2
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596
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Handling biological replicates in DESeq2
DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
5
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
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6
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943
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 10
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2
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366
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 6 weeks ago by • 0
4
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5
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616
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 weeks ago LuciaNhu • 0
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1
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389
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Average expression of genes across replicates
DESeq2
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
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0
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130
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
7 weeks ago info ▴ 10
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10
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Question about using LRT test for time course experiments with DESeq2
DESeq2
7 weeks ago • updated 6 weeks ago Denise • 0
0
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1
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340
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Deseq to output continous sequencing data
DESeq2
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
1
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4
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807
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Adjusted p-values become NA when sub-setting samples
DESeq2
10 weeks ago • updated 6 weeks ago txema.heredia • 0
3
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3
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890
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 7 weeks ago by • 0
0
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2
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349
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 8 weeks ago by • 0
0
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1
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290
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
2
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3
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1.0k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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4
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760
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DESeq2 - interactions when using factors concatenated into group
DESeq2
9 weeks ago • updated 8 weeks ago boczniak767 ▴ 740
0
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1
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203
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
9 weeks ago JY • 0
0
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1
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289
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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212
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how to extract expression matrix post deseq2
DESeq2
written 9 weeks ago by • 0
0
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2
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211
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Using Normalized Counts in DESeq2
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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2
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265
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When running contrasts, does it use normalized read counts?
DESeq2
9 weeks ago Katherine • 0
0
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1
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215
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
3
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4
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526
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
10 weeks ago Eva ▴ 10
1
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4
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508
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 9 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
0
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1
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192
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
3
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11
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764
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
2
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4
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434
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
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6
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839
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 8 weeks ago by 43k • written 10 weeks ago by • 0
5
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4
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468
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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