Showing : DESEq2 • reset
6
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2.3k
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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
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 9 days ago by • 0 • written 8.8 years ago by ▴ 30
0
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4
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236
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DEG with low counts
DESeq2
updated 8 days ago by 41k • written 13 days ago by • 0
0
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1
reply
117
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covariate with negative and positive values
DESeq2
updated 9 days ago by 41k • written 11 days ago by • 0
1
vote
2
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223
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How to retrieve detailed regression results from deseq2
DESeq2
17 days ago • updated 8 days ago Weiqian ▴ 10
1
vote
6
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407
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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
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5
replies
705
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DESeq2 setting significant p-value
DESeq2
updated 8 days ago by 41k • written 5.0 years ago by ▴ 10
0
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7
replies
391
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DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by 41k • written 10 weeks ago by • 0
0
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4
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235
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 25 days ago by 41k • written 26 days ago by • 0
0
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2
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154
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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
201
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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
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago • updated 24 days ago Layal • 0
0
votes
1
reply
124
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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
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2
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400
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago ussarizona ▴ 10
0
votes
1
reply
93
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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
100
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rlog transformation
DESeq2
updated 9 days ago by 41k • written 9 days ago by • 0
1
vote
1
reply
156
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by 65k • written 23 days ago by • 0
0
votes
2
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225
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Regressing out batch effects
DESeq2
updated 17 days ago by 41k • written 23 days ago by • 0
2
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5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 days ago by • 0 • written 10 months ago by • 0
1
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8
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1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 27 days ago by ★ 13k • written 10 months ago by ▴ 10
3
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3
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180
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
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4
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575
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 11 days ago by 41k • written 6 months 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 22 days ago by 65k • written 22 days ago by • 0
3
votes
1
reply
237
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 3 days ago by 41k • written 4 days ago by ▴ 40
1
vote
4
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211
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago winwater0928 • 0
1
vote
3
replies
141
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 20
0
votes
1
reply
88
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 3 days ago by 41k • written 3 days ago by • 0
0
votes
2
replies
119
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PCA plot suggestions
DESeq2 PCAtools
updated 1 day ago by 41k • written 2 days ago by • 0
2
votes
9
replies
286
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 2 days ago by 65k • written 2 days ago by • 0
0
votes
1
reply
121
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Bioinformatics student
Des DESeq2
updated 15 days ago by • 0 • written 15 days ago by • 0
1
vote
3
replies
126
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
3
replies
178
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 20
1
vote
2
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175
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Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago hemantcnaik • 0
0
votes
1
reply
144
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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
161
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DESeq2 gives an error and R crashes
DESeq2
16 days ago Shefali • 0
0
votes
8
replies
261
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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
4
replies
201
views
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
1
reply
115
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Deseq2 Rlog transformation
DESeq2
updated 12 days ago by ★ 4.0k • written 13 days ago by • 0
38 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
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…
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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