Showing : DESeq2 • reset
2
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5
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237
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Differential variability modelling with vst() expression
limma DESeq2
updated 4 hours ago by • 0 • written 5 days ago by • 0
0
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2
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304
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
6 days ago • updated 3 days ago sindhuri • 0
2
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8
replies
547
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
6 days ago • updated 4 days ago Quang ▴ 10
1
vote
1
reply
256
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 7 days ago by 43k • written 7 days ago by • 0
0
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1
reply
135
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 8 days ago by ★ 1.4k • written 8 days ago by • 0
0
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1
reply
326
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 days ago by 43k • written 22 days ago by • 0
2
votes
1
reply
329
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 days ago by 43k • written 19 days ago by • 0
0
votes
2
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239
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
17 days ago • updated 15 days ago Kucsera • 0
1
vote
1
reply
355
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 25 days ago by 43k • written 4 weeks ago by • 0
1
vote
9
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767
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 28 days ago by ▴ 30
0
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2
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294
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 29 days ago by ★ 4.6k • written 4 weeks ago by • 0
1
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5
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526
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Deseq2 Design
RNASeq DESeq2
updated 29 days ago by 67k • written 4 weeks ago by • 0
0
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5
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487
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p value is 0, padj is 0
DESeq2
4 weeks ago Wirayatida • 0
1
vote
2
replies
470
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
4 weeks ago georgii.vdovin • 0
0
votes
7
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771
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
1
reply
265
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 20
0
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3
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401
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DESeq2 - Comparing Comparisons
DESeq2
updated 4 weeks ago by 67k • written 5 weeks ago by • 0
0
votes
4
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522
views
lfcShrink and alpha value
lfcShrink DESeq2
6 weeks ago • updated 5 weeks ago cropero • 0
1
vote
1
reply
268
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
0
votes
2
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203
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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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260
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
7 weeks ago • updated 6 weeks ago Anna • 0
1
vote
2
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548
views
Deseq2 res Function
DESeq2
updated 7 weeks ago by 67k • written 7 weeks ago by ▴ 10
0
votes
4
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420
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
7 weeks ago NB • 0
0
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5
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437
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
votes
1
reply
244
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
1
vote
2
replies
305
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
7 weeks ago Denise • 0
0
votes
1
reply
161
views
eRNAs count
RNASeq DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
votes
1
reply
401
views
DESeq2 rerun returns different results
DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
votes
1
reply
253
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
0
votes
1
reply
237
views
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
votes
2
replies
631
views
Handling biological replicates in DESeq2
DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
1
vote
6
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1000
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 9 weeks ago by 43k • written 9 weeks ago by ▴ 10
0
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2
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387
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 9 weeks ago by • 0
4
votes
5
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673
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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
reply
409
views
Average expression of genes across replicates
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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0
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146
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
10 weeks ago info ▴ 10
0
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10
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1.4k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
11 weeks ago • updated 10 weeks ago Denise • 0
0
votes
1
reply
362
views
Deseq to output continous sequencing data
DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
vote
4
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860
views
Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 9 weeks ago txema.heredia • 0
3
votes
3
replies
938
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 weeks ago by • 0
0
votes
2
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373
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 12 weeks ago by • 0
0
votes
1
reply
314
views
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
votes
3
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1.0k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
1
vote
4
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788
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
12 weeks ago • updated 11 weeks ago boczniak767 ▴ 740
0
votes
1
reply
225
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
12 weeks ago JY • 0
0
votes
1
reply
301
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
2
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235
views
how to extract expression matrix post deseq2
DESeq2
written 3 months ago by • 0
0
votes
2
replies
229
views
Using Normalized Counts in DESeq2
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
2
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292
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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
Comment: Differential variability modelling with vst() expression by convincing.shark.jqvy • 0
Your approach to differential variability modeling using vst() looks promising! It mirrors the challenge of mastering levels in [Geometry D…
Answer: DESeq2 Heatmap by James W. MacDonald 67k
Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…
Answer: Improve performance of qusage aggregateGeneSet by James W. MacDonald 67k
This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Votes
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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