Showing : DESEQ2 • reset
1
vote
3
replies
112
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 day ago by 41k • written 1 day ago by • 0
2
votes
9
replies
278
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 1 day ago by 65k • written 2 days ago by • 0
0
votes
2
replies
110
views
PCA plot suggestions
DESeq2 PCAtools
updated 22 hours ago by 41k • written 2 days ago by • 0
0
votes
1
reply
85
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 2 days ago by 41k • written 2 days ago by • 0
1
vote
3
replies
131
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 20
1
vote
4
replies
201
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago winwater0928 • 0
3
votes
1
reply
231
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 40
0
votes
8
replies
257
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 2 days ago by ★ 1.3k • written 3 days ago by • 0
3
votes
3
replies
178
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
1
reply
98
views
rlog transformation
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
0
votes
1
reply
92
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 days ago by 41k • written 9 days ago by • 0
0
votes
4
replies
201
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 7 days ago lonn • 0
1
vote
2
replies
317
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 23 hours ago ussarizona ▴ 10
0
votes
1
reply
123
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 8 days ago by 41k • written 10 days ago by • 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
0
votes
4
replies
236
views
DEG with low counts
DESeq2
updated 8 days ago by 41k • written 12 days ago by • 0
0
votes
1
reply
114
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by ★ 4.0k • written 13 days ago by • 0
1
vote
2
replies
174
views
Design Matrix within group comparison more than two groups
DESeq2
14 days ago hemantcnaik • 0
0
votes
1
reply
121
views
Bioinformatics student
Des DESeq2
updated 14 days ago by • 0 • written 14 days ago by • 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago Shefali • 0
1
vote
2
replies
222
views
How to retrieve detailed regression results from deseq2
DESeq2
16 days ago • updated 7 days ago Weiqian ▴ 10
0
votes
1
reply
144
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 17 days ago by 41k • written 17 days 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 21 days ago by 65k • written 22 days ago by • 0
0
votes
2
replies
199
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 17 days ago by 41k • written 22 days ago by ▴ 30
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 17 days ago by 41k • written 22 days ago by • 0
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 22 days ago by 65k • written 22 days ago by • 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 23 days ago by 41k • written 23 days ago by • 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
24 days ago Layal • 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
25 days ago • updated 24 days ago michelafrancesconi8 • 0
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 24 days ago by 41k • written 25 days ago by • 0
0
votes
1
reply
146
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 29 days ago by 41k • written 29 days ago by • 0
2
votes
3
replies
333
views
PCA of different bacterial species
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by ▴ 10
3
votes
2
replies
203
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
0
votes
1
reply
163
views
collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
1
vote
2
replies
221
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
0
votes
2
replies
214
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
0
votes
3
replies
248
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
2
votes
3
replies
288
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
1
reply
136
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
169
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
1
vote
1
reply
168
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
2
votes
2
replies
212
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
6 weeks ago • updated 5 weeks ago feather-W • 0
0
votes
4
replies
409
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
2
replies
247
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
0
votes
7
replies
413
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
0
votes
2
replies
307
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
2
votes
1
reply
237
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
211
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
vote
1
reply
198
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
France, 2 minutes ago
WEHI, Melbourne, Australia, 4 minutes ago
Ireland, 1 hour ago
United States, 1 hour ago
Belgium, 2 hours ago
Traffic: 596 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