Showing : DEseq2 • reset
0
votes
2
replies
10
views
Different Shrunk Log2FC according with reference
DESeq2
24 minutes ago • updated 11 minutes ago andrebolerbarros ▴ 20
0
votes
3
replies
61
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 40 minutes ago by ★ 4.0k • written 17 hours ago by • 0
0
votes
0
replies
9
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
58 minutes ago winwater0928 • 0
1
vote
1
reply
83
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 6 hours ago by 41k • written 14 hours ago by ▴ 40
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 18 hours ago by 41k • written 4.6 years ago by ▴ 10
3
votes
3
replies
137
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 hours ago by 41k • written 1 day ago by • 0
0
votes
4
replies
188
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 days ago • updated 4 days ago lonn • 0
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago Weiqian ▴ 10
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by 41k • written 9 weeks ago by • 0
2
votes
5
replies
693
views
DESeq2 setting significant p-value
DESeq2
updated 4 days ago by 41k • written 5.0 years ago by ▴ 10
0
votes
4
replies
227
views
DEG with low counts
DESeq2
updated 4 days ago by 41k • written 9 days ago by • 0
0
votes
1
reply
84
views
rlog transformation
DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
83
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
1
reply
93
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
107
views
covariate with negative and positive values
DESeq2
updated 5 days ago by 41k • written 7 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 days ago by • 0 • written 8.8 years ago by ▴ 30
0
votes
1
reply
109
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by ★ 4.0k • written 6 days ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
563
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 days ago by 41k • written 6 months ago by • 0
0
votes
3
replies
170
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 7 days ago by 41k • written 8 days ago by ▴ 20
0
votes
1
reply
108
views
Deseq2 Rlog transformation
DESeq2
updated 8 days ago by ★ 4.0k • written 10 days ago by • 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
11 days ago • updated 10 days ago hemantcnaik • 0
0
votes
1
reply
115
views
Bioinformatics student
Des DESeq2
updated 11 days ago by • 0 • written 11 days ago by • 0
0
votes
1
reply
152
views
DESeq2 gives an error and R crashes
DESeq2
13 days ago • updated 12 days ago Shefali • 0
0
votes
2
replies
191
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 14 days ago by 41k • written 18 days ago by ▴ 30
0
votes
1
reply
135
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 14 days ago by 41k • written 14 days ago by • 0
0
votes
2
replies
219
views
Regressing out batch effects
DESeq2
updated 14 days ago by 41k • written 19 days ago by • 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 days ago by 65k • written 18 days ago by • 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 19 days ago by 65k • written 19 days ago by • 0
1
vote
6
replies
400
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 20 days ago by 41k • written 20 days ago by • 0
0
votes
2
replies
149
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 days ago michelafrancesconi8 • 0
1
vote
1
reply
135
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
21 days ago Layal • 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 21 days ago by 41k • written 22 days ago by • 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 23 days ago by ★ 13k • written 9 months ago by ▴ 10
0
votes
1
reply
140
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 26 days ago by 41k • written 26 days ago by • 0
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 27 days ago Chanderkant Chaudhary • 0
2
votes
3
replies
320
views
PCA of different bacterial species
DESeq2
updated 27 days ago by 41k • written 28 days ago by ▴ 10
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 28 days ago fr8712ca-s • 0
0
votes
1
reply
157
views
collapseReplicates dimension error
DESeq2 Dese
updated 29 days ago by 41k • written 4 weeks ago by • 0
3
votes
2
replies
196
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
29 days ago Anita ▴ 10
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago kcarey • 0
2
votes
3
replies
282
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by 41k • written 5 weeks ago by ▴ 20
0
votes
3
replies
242
views
Help with Complex DESeq2 Design
DESeq2
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
4
votes
7
replies
675
views
DESeq2 unable to handle large count values
DESeq2
updated 5 weeks ago by 41k • written 5 months ago by • 0
1
vote
1
reply
163
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
163
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
votes
2
replies
206
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
1
vote
3
replies
367
views
DEseq2 coefficient
DESeq2 coefficient
8 weeks ago • updated 5 weeks ago JKim • 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 5 weeks ago by • 0 • written 12 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio by ATpoint ★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Awards • All
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
Popular Question to i.sudbery ▴ 40
Scholar to Michael Love 41k
Popular Question to shepherl 3.8k
Locations • All
Helsinki, just now
Italy, 1 minute ago
Japan, 2 minutes ago
Germany, 3 minutes ago
South Korea, 8 minutes ago
Traffic: 884 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