Showing : DEseq2 • reset
0
votes
1
reply
56
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
updated 1 day ago by ★ 4.6k • written 1 day ago by • 0
0
votes
0
replies
55
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
3 days ago KR • 0
0
votes
0
replies
85
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
6 days ago Jimmy Mak • 0
1
vote
1
reply
277
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 10 days ago by 43k • written 19 days ago by • 0
1
vote
9
replies
723
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 days ago by ▴ 30
0
votes
2
replies
254
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 days ago by ★ 4.6k • written 18 days ago by • 0
1
vote
5
replies
470
views
Deseq2 Design
RNASeq DESeq2
updated 13 days ago by 67k • written 17 days ago by • 0
0
votes
5
replies
422
views
p value is 0, padj is 0
DESeq2
18 days ago • updated 17 days ago Wirayatida • 0
1
vote
2
replies
424
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
19 days ago • updated 18 days ago georgii.vdovin • 0
0
votes
7
replies
705
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 19 days ago by • 0 • written 21 days ago by • 0
0
votes
1
reply
242
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 23 days ago by 43k • written 23 days ago by ▴ 20
0
votes
3
replies
349
views
DESeq2 - Comparing Comparisons
DESeq2
updated 18 days ago by 67k • written 25 days ago by • 0
0
votes
4
replies
481
views
lfcShrink and alpha value
lfcShrink DESeq2
4 weeks ago • updated 25 days ago cropero • 0
1
vote
1
reply
242
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 27 days ago by 43k • written 4 weeks ago by • 0
0
votes
2
replies
173
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 27 days ago by 43k • written 28 days ago by • 0
0
votes
2
replies
247
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
4 weeks ago Anna • 0
1
vote
2
replies
529
views
Deseq2 res Function
DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by ▴ 10
0
votes
4
replies
401
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
5 weeks ago NB • 0
0
votes
5
replies
401
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
0
votes
1
reply
227
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
1
vote
2
replies
291
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
5 weeks ago Denise • 0
0
votes
1
reply
150
views
eRNAs count
RNASeq DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
0
votes
1
reply
392
views
DESeq2 rerun returns different results
DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
0
votes
1
reply
232
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
0
votes
1
reply
221
views
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
2
votes
2
replies
606
views
Handling biological replicates in DESeq2
DESeq2
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
1
vote
6
replies
961
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 10
0
votes
2
replies
377
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 7 weeks ago by • 0
4
votes
5
replies
645
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
7 weeks ago LuciaNhu • 0
0
votes
1
reply
396
views
Average expression of genes across replicates
DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
votes
0
replies
138
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
8 weeks ago info ▴ 10
0
votes
10
replies
1.3k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
8 weeks ago • updated 7 weeks ago Denise • 0
0
votes
1
reply
348
views
Deseq to output continous sequencing data
DESeq2
updated 8 weeks ago by 43k • written 11 weeks ago by • 0
1
vote
4
replies
825
views
Adjusted p-values become NA when sub-setting samples
DESeq2
11 weeks ago • updated 7 weeks ago txema.heredia • 0
3
votes
3
replies
910
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 9 weeks ago by • 0
0
votes
2
replies
359
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 9 weeks ago by • 0
0
votes
1
reply
302
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
2
votes
3
replies
1.0k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
1
vote
4
replies
772
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
10 weeks ago • updated 9 weeks ago boczniak767 ▴ 740
0
votes
1
reply
212
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
10 weeks ago JY • 0
0
votes
1
reply
294
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
votes
2
replies
217
views
how to extract expression matrix post deseq2
DESeq2
written 10 weeks ago by • 0
0
votes
2
replies
219
views
Using Normalized Counts in DESeq2
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
1
vote
2
replies
274
views
When running contrasts, does it use normalized read counts?
DESeq2
11 weeks ago Katherine • 0
0
votes
1
reply
229
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
3
votes
4
replies
548
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
11 weeks ago Eva ▴ 10
1
vote
4
replies
528
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 10 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
0
votes
1
reply
201
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
3
votes
11
replies
784
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to rohitsatyam102 ▴ 20
Popular Question to Hervé Pagès 16k
Teacher to dsull ▴ 40
Locations • All
University of Cambridge, UK | NIH Bethesda, MD, 20 minutes ago
United States, 43 minutes ago
Sweden, 1 hour ago
India, 1 hour ago
United States, 2 hours ago
Traffic: 600 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