Showing : DESEq2 • reset
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
1 day ago Jimmy Mak • 0
1
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1
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168
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 days ago by 43k • written 13 days ago by • 0
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9
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667
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 7 days ago by ▴ 30
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2
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239
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 7 days ago by ★ 4.6k • written 12 days ago by • 0
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5
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456
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Deseq2 Design
RNASeq DESeq2
updated 8 days ago by 67k • written 12 days ago by • 0
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5
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408
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p value is 0, padj is 0
DESeq2
12 days ago Wirayatida • 0
1
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2
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411
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 days ago • updated 12 days ago georgii.vdovin • 0
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7
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687
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 days ago by • 0 • written 15 days ago by • 0
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1
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237
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 17 days ago by 43k • written 18 days ago by ▴ 20
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3
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336
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DESeq2 - Comparing Comparisons
DESeq2
updated 13 days ago by 67k • written 20 days ago by • 0
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4
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464
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lfcShrink and alpha value
lfcShrink DESeq2
25 days ago • updated 20 days ago cropero • 0
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1
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232
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 22 days ago by 43k • written 29 days ago by • 0
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2
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166
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 22 days ago by 43k • written 22 days ago by • 0
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2
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233
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
28 days ago • updated 27 days ago Anna • 0
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2
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513
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Deseq2 res Function
DESeq2
updated 29 days ago by 67k • written 4 weeks ago by ▴ 10
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4
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393
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
4 weeks ago NB • 0
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5
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388
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Identical samples after deseq2 batch effect removal
DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
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1
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224
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 4 weeks ago by 67k • written 4 weeks ago by • 0
1
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2
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284
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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
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144
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eRNAs count
RNASeq DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
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1
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389
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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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226
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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
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1
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208
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
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2
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599
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Handling biological replicates in DESeq2
DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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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 6.0 years ago by ▴ 30
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6
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947
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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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373
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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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625
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
7 weeks ago LuciaNhu • 0
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1
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392
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Average expression of genes across replicates
DESeq2
updated 7 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
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135
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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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1.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
8 weeks ago • updated 7 weeks ago Denise • 0
0
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1
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343
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Deseq to output continous sequencing data
DESeq2
updated 8 weeks ago by 43k • written 10 weeks ago by • 0
1
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4
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813
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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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894
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 8 weeks ago by • 0
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2
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353
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 9 weeks ago by • 0
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1
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295
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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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
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4
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765
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DESeq2 - interactions when using factors concatenated into group
DESeq2
9 weeks ago • updated 8 weeks ago boczniak767 ▴ 740
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1
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206
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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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291
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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
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2
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214
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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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214
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Using Normalized Counts in DESeq2
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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2
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269
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When running contrasts, does it use normalized read counts?
DESeq2
10 weeks ago Katherine • 0
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1
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222
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
3
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4
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537
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
10 weeks ago Eva ▴ 10
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4
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516
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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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197
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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 11 weeks ago by • 0
3
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11
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767
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 weeks ago by • 0
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4
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439
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
11 weeks ago jihoon.kim.1495 ▴ 10
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6
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842
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 8 weeks ago by 43k • written 11 weeks ago by • 0
50 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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