Showing : Deseq2 • reset
2
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Differential variability modelling with vst() expression
limma DESeq2
written 9 days ago by • 0
0
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2
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338
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
10 days ago • updated 7 days ago sindhuri • 0
2
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9
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697
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
updated 3 days ago by 43k • written 10 days ago by ▴ 10
1
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1
reply
266
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 11 days ago by 43k • written 11 days ago by • 0
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1
reply
146
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 12 days ago by ★ 1.4k • written 12 days ago by • 0
0
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1
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331
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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
updated 15 days ago by 43k • written 25 days ago by • 0
2
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1
reply
334
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 15 days ago by 43k • written 22 days ago by • 0
0
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2
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249
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
21 days ago • updated 19 days ago Kucsera • 0
1
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1
reply
359
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 29 days ago by 43k • written 5 weeks ago by • 0
1
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9
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797
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 weeks ago by ▴ 30
0
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2
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303
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
1
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5
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553
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Deseq2 Design
RNASeq DESeq2
updated 4 weeks ago by 67k • written 5 weeks ago by • 0
0
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5
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496
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p value is 0, padj is 0
DESeq2
5 weeks ago Wirayatida • 0
1
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2
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475
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago georgii.vdovin • 0
0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
0
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1
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271
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 20
0
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3
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408
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DESeq2 - Comparing Comparisons
DESeq2
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
0
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4
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534
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lfcShrink and alpha value
lfcShrink DESeq2
7 weeks ago • updated 6 weeks ago cropero • 0
1
vote
1
reply
277
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
0
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2
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212
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
0
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2
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262
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
7 weeks ago Anna • 0
1
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2
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553
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Deseq2 res Function
DESeq2
updated 7 weeks ago by 67k • written 8 weeks ago by ▴ 10
0
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4
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425
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
8 weeks ago NB • 0
0
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5
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443
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Identical samples after deseq2 batch effect removal
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
0
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1
reply
249
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
1
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2
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307
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
8 weeks ago Denise • 0
0
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1
reply
166
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eRNAs count
RNASeq DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
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1
reply
403
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DESeq2 rerun returns different results
DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
0
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1
reply
255
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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1
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241
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
2
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2
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637
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Handling biological replicates in DESeq2
DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
5
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2
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26k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
1
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6
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1.0k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 10
0
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2
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390
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 10 weeks ago by • 0
4
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5
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677
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 weeks ago LuciaNhu • 0
0
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1
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412
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Average expression of genes across replicates
DESeq2
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
0
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0
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150
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
11 weeks ago info ▴ 10
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10
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1.4k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
11 weeks ago • updated 10 weeks ago Denise • 0
0
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1
reply
364
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Deseq to output continous sequencing data
DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
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4
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866
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 10 weeks ago txema.heredia • 0
3
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3
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944
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 weeks ago by • 0
0
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2
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374
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 12 weeks ago by • 0
0
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1
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320
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
2
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3
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1.1k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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4
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794
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DESeq2 - interactions when using factors concatenated into group
DESeq2
3 months ago • updated 12 weeks ago boczniak767 ▴ 740
0
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1
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230
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
3 months ago JY • 0
0
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1
reply
306
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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2
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237
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how to extract expression matrix post deseq2
DESeq2
written 3 months ago by • 0
0
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2
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231
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Using Normalized Counts in DESeq2
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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2
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295
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When running contrasts, does it use normalized read counts?
DESeq2
3 months ago Katherine • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Curiously shaped volcano plot with using oarfish + swish to do differential gene by Michael Love 43k
See swish vignette, these are explained.
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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