Showing : Deseq2 • reset
0
votes
2
replies
77
views
PCA plot suggestions
DESeq2 PCAtools
updated 2 hours ago by 41k • written 1 day ago by • 0
1
vote
2
replies
126
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 3 hours ago ussarizona ▴ 10
1
vote
3
replies
73
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 4 hours ago by 41k • written 22 hours ago by • 0
1
vote
4
replies
181
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 11 hours ago winwater0928 • 0
2
votes
9
replies
262
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 hours ago by 65k • written 1 day ago by • 0
0
votes
8
replies
241
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 3 days ago by • 0
0
votes
1
reply
80
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 2 days ago by • 0
1
vote
3
replies
111
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 20
3
votes
1
reply
221
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
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 3 days ago by 41k • written 4.6 years ago by ▴ 10
3
votes
3
replies
172
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 6 days ago lonn • 0
1
vote
2
replies
221
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago Weiqian ▴ 10
0
votes
7
replies
390
views
DESeq filtering specific to contrasts
DESeq2
updated 7 days ago by 41k • written 10 weeks ago by • 0
2
votes
5
replies
701
views
DESeq2 setting significant p-value
DESeq2
updated 7 days ago by 41k • written 5.0 years ago by ▴ 10
0
votes
4
replies
233
views
DEG with low counts
DESeq2
updated 7 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
94
views
rlog transformation
DESeq2
updated 8 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 8 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
115
views
covariate with negative and positive values
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 30
0
votes
1
reply
121
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
573
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
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 10 days ago by 41k • written 11 days ago by ▴ 20
0
votes
1
reply
112
views
Deseq2 Rlog transformation
DESeq2
updated 11 days ago by ★ 4.0k • written 12 days ago by • 0
1
vote
2
replies
171
views
Design Matrix within group comparison more than two groups
DESeq2
14 days ago • updated 13 days ago hemantcnaik • 0
0
votes
1
reply
119
views
Bioinformatics student
Des DESeq2
updated 14 days ago by • 0 • written 14 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
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
1
reply
143
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 16 days ago by 41k • written 17 days ago by • 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 16 days ago by 41k • written 22 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 21 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 22 days ago by 41k • written 23 days ago by • 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
24 days ago • updated 23 days ago michelafrancesconi8 • 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
24 days ago • updated 23 days ago Layal • 0
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 24 days ago by 41k • written 24 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
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
1
vote
2
replies
218
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
2
votes
3
replies
329
views
PCA of different bacterial species
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by ▴ 10
0
votes
7
replies
412
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
0
votes
1
reply
161
views
collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
3
votes
2
replies
202
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
0
votes
2
replies
213
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
2
votes
3
replies
287
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
247
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
4
votes
7
replies
682
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
166
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
134
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
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…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
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)
biomaRt error: database disk image is malformed
Awards • All
Popular Question to shepherl 3.8k
Popular Question to James W. MacDonald 65k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Locations • All
France, 12 minutes ago
Melbourne, Australia, 24 minutes ago
Canada, 33 minutes ago
Canada, 45 minutes ago
United States, 54 minutes ago
Traffic: 885 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