Showing : DESeq2 • reset
3
votes
2
replies
227
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 days ago by 64k • written 5 days ago by • 0
0
votes
3
replies
162
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
11 days ago • updated 3 days ago Karthik • 0
0
votes
3
replies
149
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 days ago Oenone • 0
1
vote
1
reply
82
views
Lower FDR cutoff gives more gene counts
DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
154
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 6 days ago by 41k • written 9 days ago by • 0
1
vote
1
reply
138
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 6 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
127
views
How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 6 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
124
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 6 days ago by 41k • written 9 days ago by • 0
0
votes
2
replies
102
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
11 days ago • updated 2 days ago yee • 0
0
votes
2
replies
154
views
Batch correction where one of the batches only has a single sample
DESeq2
9 days ago • updated 6 days ago Tom ▴ 10
0
votes
3
replies
203
views
Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
9 days ago • updated 6 days ago claire • 0
2
votes
3
replies
148
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
10 days ago • updated 5 days ago Karthik • 0
0
votes
1
reply
125
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 12 days ago by 41k • written 17 days ago by • 0
2
votes
2
replies
173
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
13 days ago • updated 12 days ago Manthos • 0
1
vote
4
replies
239
views
Can DESeq2 be used to compare groups of genes?
DESeq2
13 days ago • updated 12 days ago pl23 • 0
0
votes
2
replies
187
views
Predicting missing values splines DESeq2
deseq DESeq2
16 days ago • updated 13 days ago georgii.vdovin • 0
0
votes
1
reply
140
views
DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 18 days ago by ★ 3.6k • written 18 days ago by • 0
0
votes
2
replies
212
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
20 days ago • updated 19 days ago anton.kratz ▴ 60
4
votes
6
replies
385
views
weird volcano plot
DESeq2
updated 20 days ago by ★ 3.6k • written 24 days ago by ▴ 10
0
votes
1
reply
176
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 18 days ago by 13k • written 23 days ago by • 0
3
votes
5
replies
290
views
DESeq2 unable to handle large count values
DESeq2
updated 24 days ago by ★ 3.6k • written 25 days ago by • 0
2
votes
5
replies
341
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 25 days ago by 41k • written 26 days ago by • 0
0
votes
1
reply
218
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 26 days ago by 41k • written 6 weeks ago by • 0
0
votes
1
reply
209
views
DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 26 days ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
162
views
Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 26 days ago by 41k • written 27 days ago by • 0
0
votes
2
replies
188
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
26 days ago • updated 25 days ago Ben • 0
0
votes
9
replies
2.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 26 days ago by • 0 • written 6.1 years ago by ▴ 60
0
votes
2
replies
198
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
28 days ago • updated 26 days ago RHEA • 0
1
vote
1
reply
165
views
DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 29 days ago by ★ 3.6k • written 29 days ago by ▴ 20
0
votes
7
replies
654
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 27 days ago by 64k • written 4 weeks ago by • 0
0
votes
3
replies
226
views
DESeq2: FPMs varying based on sample groups used
DESeq2
updated 27 days ago by ★ 3.6k • written 4 weeks ago by • 0
0
votes
8
replies
518
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
4 weeks ago • updated 27 days ago Luca • 0
0
votes
1
reply
172
views
Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 4 weeks ago by ▴ 740 • written 5 weeks ago by • 0
2
votes
10
replies
647
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
5 weeks ago • updated 28 days ago rohitsatyam102 ▴ 20
0
votes
6
replies
377
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 weeks ago erika.maldonado-rosado • 0
0
votes
2
replies
277
views
How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
2
replies
240
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
5 weeks ago Crystal571 • 0
2
votes
3
replies
416
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 5 weeks ago by ★ 1.3k • written 5 weeks ago by • 0
0
votes
2
replies
314
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
6 weeks ago • updated 5 weeks ago Roey Angel • 0
0
votes
2
replies
385
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 weeks ago • updated 5 weeks ago Karthik • 0
0
votes
1
reply
255
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 6 weeks ago by 41k • written 7 weeks ago by • 0
0
votes
0
replies
134
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 weeks ago Florian • 0
0
votes
1
reply
178
views
choosing rank for GSEA
gsea DESeq2
updated 6 weeks ago by ★ 3.6k • written 6 weeks ago by • 0
1
vote
1
reply
218
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 weeks ago by 64k • written 6 weeks ago by • 0
0
votes
3
replies
234
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
1
vote
11
replies
557
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 weeks ago by 41k • written 7 weeks ago by • 0
0
votes
2
replies
208
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
7 weeks ago • updated 6 weeks ago georgii.vdovin • 0
3
votes
5
replies
477
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 6 weeks ago by 41k • written 7 weeks ago by • 0
0
votes
1
reply
219
views
DeSeq2 normalization 16S
DESeq2
updated 7 weeks ago by 41k • written 7 weeks ago by • 0
0
votes
4
replies
325
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
8 weeks ago • updated 6 weeks ago ar14g12 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: RNASeq time course analysis, missing time points for control by Gordon Smyth 48k
You could fit a spline trend with design matrix `treatment+spline`. Then it won't matter than the control and treatment times don't match u…
Comment: DESeq2 - groups with biological replicates from the same patient by Oscar • 0
Thanks James for your helpful response. This particular experimental set up is very common in iPSC studies, where multiple differentiations…
Comment: DESeq2 test for synergistic vs additive effects by Jay • 0
Why is TrtAB - TrtA - TrtB + Control "not really a thing"? i came to this forum answer when attempting to use EdgeR to answer a similar que…
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Votes
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Awards • All
Popular Question to Poonam • 0
Scholar to James W. MacDonald 64k
Scholar to Assa Yeroslaviz ★ 1.5k
Popular Question to Gordon Smyth 48k
Popular Question to Endre Sebestyén ▴ 70
Locations • All
Melbourne, Australia, 4 minutes ago
United Kingdom, 12 minutes ago
WEHI, Melbourne, Australia, 35 minutes ago
WEHI, Melbourne, Australia, 36 minutes ago
The city by the bay, 1 hour ago
Traffic: 535 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