Showing : DESeq2 • reset
0
votes
1
reply
138
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 1 day ago by 43k • written 10 days ago by • 0
1
vote
8
replies
574
views
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
0
votes
2
replies
226
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 4 days ago by ★ 4.6k • written 8 days ago by • 0
1
vote
5
replies
429
views
Deseq2 Design
RNASeq DESeq2
updated 4 days ago by 67k • written 8 days ago by • 0
0
votes
5
replies
382
views
p value is 0, padj is 0
DESeq2
9 days ago • updated 8 days ago Wirayatida • 0
1
vote
2
replies
402
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 days ago georgii.vdovin • 0
0
votes
7
replies
670
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 days ago by • 0 • written 11 days ago by • 0
0
votes
1
reply
231
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 days ago by 43k • written 14 days ago by ▴ 20
0
votes
3
replies
329
views
DESeq2 - Comparing Comparisons
DESeq2
updated 9 days ago by 67k • written 16 days ago by • 0
0
votes
4
replies
456
views
lfcShrink and alpha value
lfcShrink DESeq2
22 days ago • updated 16 days ago cropero • 0
1
vote
1
reply
228
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 18 days ago by 43k • written 25 days ago by • 0
0
votes
2
replies
158
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 18 days ago by 43k • written 18 days ago by • 0
0
votes
2
replies
229
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
24 days ago • updated 23 days ago Anna • 0
1
vote
2
replies
507
views
Deseq2 res Function
DESeq2
updated 25 days ago by 67k • written 27 days ago by ▴ 10
0
votes
4
replies
382
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
28 days ago NB • 0
0
votes
5
replies
377
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 29 days ago by 43k • written 29 days ago by • 0
0
votes
1
reply
217
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 29 days ago by 67k • written 29 days ago by • 0
1
vote
2
replies
278
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
4 weeks ago Denise • 0
0
votes
1
reply
138
views
eRNAs count
RNASeq DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
0
votes
1
reply
387
views
DESeq2 rerun returns different results
DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
0
votes
1
reply
225
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
0
votes
1
reply
191
views
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
votes
2
replies
596
views
Handling biological replicates in DESeq2
DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
vote
6
replies
943
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 10
0
votes
2
replies
366
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 6 weeks ago by • 0
4
votes
5
replies
616
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 weeks ago LuciaNhu • 0
0
votes
1
reply
387
views
Average expression of genes across replicates
DESeq2
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
0
votes
0
replies
130
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
7 weeks ago info ▴ 10
0
votes
10
replies
1.3k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
7 weeks ago • updated 6 weeks ago Denise • 0
0
votes
1
reply
339
views
Deseq to output continous sequencing data
DESeq2
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
1
vote
4
replies
806
views
Adjusted p-values become NA when sub-setting samples
DESeq2
10 weeks ago • updated 6 weeks ago txema.heredia • 0
3
votes
3
replies
890
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 7 weeks ago by • 0
0
votes
2
replies
349
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 8 weeks ago by • 0
0
votes
1
reply
288
views
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
votes
3
replies
1.0k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
1
vote
4
replies
760
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
9 weeks ago • updated 8 weeks ago boczniak767 ▴ 740
0
votes
1
reply
203
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
9 weeks ago JY • 0
0
votes
1
reply
288
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
2
replies
212
views
how to extract expression matrix post deseq2
DESeq2
written 9 weeks ago by • 0
0
votes
2
replies
211
views
Using Normalized Counts in DESeq2
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
vote
2
replies
265
views
When running contrasts, does it use normalized read counts?
DESeq2
9 weeks ago Katherine • 0
0
votes
1
reply
214
views
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
votes
4
replies
526
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
10 weeks ago Eva ▴ 10
1
vote
4
replies
508
views
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
votes
1
reply
192
views
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
votes
11
replies
763
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
2
votes
4
replies
433
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
0
votes
6
replies
839
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
5
votes
4
replies
468
views
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
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
30 N Gould St STE 39034 Sheridan, WY, 1 hour ago
Pakistan, 2 hours ago
Germany, 5 hours ago
Barcelona/Universitat Pompeu Fabra, 5 hours ago
Traffic: 482 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6