Showing : Deseq2 • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 7 days ago by • 0 • written 8.8 years ago by ▴ 30
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by 41k • written 4.6 years ago by ▴ 10
3
votes
1
reply
215
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 40
3
votes
3
replies
172
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
2
votes
5
replies
700
views
DESeq2 setting significant p-value
DESeq2
updated 6 days ago by 41k • written 5.0 years ago by ▴ 10
2
votes
3
replies
329
views
PCA of different bacterial species
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 days ago by • 0 • written 10 months ago by • 0
2
votes
9
replies
254
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 16 hours ago by 65k • written 23 hours ago by • 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 22 days ago by 41k • written 22 days ago by • 0
1
vote
2
replies
216
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 29 days ago Chanderkant Chaudhary • 0
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago Weiqian ▴ 10
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by 65k • written 21 days ago by • 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 25 days ago by ★ 13k • written 10 months ago by ▴ 10
1
vote
4
replies
168
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 5 hours ago winwater0928 • 0
1
vote
3
replies
105
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 20
1
vote
2
replies
37
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 14 minutes ago by ▴ 10 • written 16 hours ago by • 0
1
vote
2
replies
171
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago hemantcnaik • 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago Layal • 0
0
votes
1
reply
143
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 16 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
159
views
DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago Shefali • 0
0
votes
1
reply
115
views
covariate with negative and positive values
DESeq2
updated 7 days ago by 41k • written 9 days ago by • 0
0
votes
4
replies
572
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 days ago by 41k • written 6 months ago by • 0
0
votes
2
replies
148
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 20 days ago by 65k • written 20 days ago by • 0
0
votes
7
replies
389
views
DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by 41k • written 10 weeks ago by • 0
0
votes
4
replies
234
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 23 days ago by 41k • written 24 days ago by • 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago michelafrancesconi8 • 0
0
votes
1
reply
144
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by 41k • written 28 days ago by • 0
0
votes
8
replies
237
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 2 days ago by • 0
0
votes
1
reply
78
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
1
reply
64
views
PCA plot suggestions
DESeq2 PCAtools
updated 22 hours ago by • 0 • written 1 day ago by • 0
0
votes
4
replies
230
views
DEG with low counts
DESeq2
updated 7 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
118
views
Bioinformatics student
Des DESeq2
updated 13 days ago by • 0 • written 13 days ago by • 0
0
votes
2
replies
197
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 16 days ago by 41k • written 21 days ago by ▴ 30
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 20
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 6 days ago lonn • 0
0
votes
1
reply
99
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
91
views
rlog transformation
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
112
views
Deseq2 Rlog transformation
DESeq2
updated 11 days ago by ★ 4.0k • written 12 days ago by • 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
0
votes
1
reply
120
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by ★ 4.0k • written 8 days ago by • 0
41 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
Germany, just now
Pakistan, 2 minutes ago
United States, 5 minutes ago
Belgium, 9 minutes ago
Spain, 9 minutes ago
Traffic: 907 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