Showing : DESEq2 • reset
6
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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 4 days ago by 41k • written 4.6 years ago by ▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 9 days ago by • 0 • written 8.8 years ago by ▴ 30
2
votes
9
replies
279
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
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 26 days ago by ★ 13k • written 10 months ago by ▴ 10
0
votes
8
replies
258
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 2 days ago by ★ 1.3k • written 4 days ago by • 0
0
votes
7
replies
391
views
DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by 41k • written 10 weeks 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 24 days ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 days ago by • 0 • written 10 months ago by • 0
2
votes
5
replies
705
views
DESeq2 setting significant p-value
DESeq2
updated 8 days ago by 41k • written 5.0 years ago by ▴ 10
0
votes
4
replies
235
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by 41k • written 25 days ago by • 0
0
votes
4
replies
201
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
10 days ago • updated 7 days ago lonn • 0
0
votes
4
replies
236
views
DEG with low counts
DESeq2
updated 8 days ago by 41k • written 12 days ago by • 0
1
vote
4
replies
203
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago winwater0928 • 0
0
votes
4
replies
574
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 10 days ago by 41k • written 6 months ago by • 0
1
vote
3
replies
134
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 20
3
votes
3
replies
178
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
1
vote
3
replies
116
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
3
replies
177
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 20
0
votes
2
replies
111
views
PCA plot suggestions
DESeq2 PCAtools
updated 1 day ago by 41k • written 2 days ago by • 0
1
vote
2
replies
175
views
Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago hemantcnaik • 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 22 days ago by 65k • written 22 days ago by • 0
1
vote
2
replies
358
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago ussarizona ▴ 10
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
2
replies
225
views
Regressing out batch effects
DESeq2
updated 17 days ago by 41k • written 23 days ago by • 0
1
vote
2
replies
223
views
How to retrieve detailed regression results from deseq2
DESeq2
16 days ago • updated 7 days ago Weiqian ▴ 10
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
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago • updated 24 days ago Layal • 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
16 days ago • updated 15 days ago Shefali • 0
0
votes
1
reply
144
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 17 days ago by 41k • written 18 days ago by • 0
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
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by 65k • written 23 days ago by • 0
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
98
views
rlog transformation
DESeq2
updated 9 days ago by 41k • written 9 days ago by • 0
3
votes
1
reply
233
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
1
reply
92
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 days ago by 41k • written 9 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
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 3 days ago by • 0
0
votes
1
reply
115
views
Deseq2 Rlog transformation
DESeq2
updated 12 days ago by ★ 4.0k • written 13 days ago by • 0
0
votes
1
reply
121
views
Bioinformatics student
Des DESeq2
updated 15 days ago by • 0 • written 15 days ago by • 0
39 results • Page 1 of 1
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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)
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