Showing : deseq2 • reset
2
votes
5
replies
75
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
4 hours ago • updated 51 minutes ago Alexandre • 0
0
votes
1
reply
42
views
PCA plot suggestions
DESeq2 PCAtools
updated 2 hours ago by • 0 • written 13 hours ago by • 0
0
votes
1
reply
73
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 hours ago by 41k • written 23 hours ago by • 0
1
vote
3
replies
89
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 20
0
votes
3
replies
109
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 4 hours ago by 65k • written 1 day ago by • 0
3
votes
1
reply
189
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 40
0
votes
8
replies
225
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 hours ago by ★ 1.3k • written 2 days ago by • 0
3
votes
3
replies
157
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 7 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
97
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
113
views
covariate with negative and positive values
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
116
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by ★ 4.0k • written 8 days ago by • 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 5 days ago lonn • 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 20
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by ★ 4.0k • written 11 days ago by • 0
1
vote
2
replies
164
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago hemantcnaik • 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
1
reply
156
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
0
votes
2
replies
194
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 20 days ago by ▴ 30
0
votes
1
reply
141
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 16 days ago by • 0
0
votes
2
replies
222
views
Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 21 days ago by • 0
0
votes
2
replies
143
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
1
vote
1
reply
153
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by 65k • written 21 days ago by • 0
1
vote
6
replies
403
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 22 days ago by • 0
1
vote
1
reply
138
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago • updated 22 days ago Layal • 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago • updated 22 days ago michelafrancesconi8 • 0
0
votes
4
replies
232
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
2
votes
3
replies
325
views
PCA of different bacterial species
DESeq2
updated 29 days ago by 41k • written 29 days ago by ▴ 10
0
votes
1
reply
159
views
collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
3
votes
2
replies
201
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 29 days ago Chanderkant Chaudhary • 0
0
votes
2
replies
211
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
2
votes
3
replies
285
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 20
0
votes
3
replies
243
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
vote
1
reply
164
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
133
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
165
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
208
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
0
votes
2
replies
302
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
4
replies
406
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
7
replies
409
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
0
votes
2
replies
240
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
vote
1
reply
207
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
2
votes
1
reply
234
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
vote
1
reply
195
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
votes
3
replies
359
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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
Canada, 1 minute ago
United States, 6 minutes ago
United States, 12 minutes ago
United States, 13 minutes ago
France, 17 minutes ago
Traffic: 1080 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