Showing : Deseq2 • reset
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
4 hours ago • updated 57 minutes ago Alexandre • 0
0
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1
reply
42
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PCA plot suggestions
DESeq2 PCAtools
updated 2 hours ago by • 0 • written 13 hours ago by • 0
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1
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73
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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
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3
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89
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Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 20
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3
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109
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 4 hours ago by 65k • written 1 day ago by • 0
3
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1
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189
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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
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8
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225
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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
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3
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157
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
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1
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89
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rlog transformation
DESeq2
updated 7 days ago by 41k • written 7 days ago by • 0
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1
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86
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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
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4
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194
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 days ago • updated 5 days ago lonn • 0
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1
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
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1
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116
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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
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1
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113
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covariate with negative and positive values
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
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3
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176
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 20
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4
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229
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DEG with low counts
DESeq2
updated 6 days ago by 41k • written 10 days ago by • 0
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1
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109
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Deseq2 Rlog transformation
DESeq2
updated 10 days ago by ★ 4.0k • written 11 days ago by • 0
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2
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164
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Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago hemantcnaik • 0
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1
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118
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Bioinformatics student
Des DESeq2
updated 13 days ago by • 0 • written 13 days ago by • 0
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1
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156
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DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
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2
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220
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How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
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1
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141
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 16 days ago by • 0
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2
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143
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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
0
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2
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194
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 20 days ago by ▴ 30
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2
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222
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Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 21 days ago by • 0
1
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1
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153
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DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by 65k • written 21 days ago by • 0
1
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6
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403
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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
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1
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138
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago • updated 22 days ago Layal • 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
23 days ago • updated 22 days ago michelafrancesconi8 • 0
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4
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232
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
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142
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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
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3
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325
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PCA of different bacterial species
DESeq2
updated 29 days ago by 41k • written 29 days ago by ▴ 10
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212
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 29 days ago Chanderkant Chaudhary • 0
0
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7
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387
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DESeq filtering specific to contrasts
DESeq2
updated 6 days ago by 41k • written 9 weeks ago by • 0
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4
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569
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 days ago by 41k • written 6 months ago by • 0
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8
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 24 days ago by ★ 13k • written 9 months ago by ▴ 10
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 days ago by • 0 • written 10 months ago by • 0
6
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16
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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 2 days ago by 41k • written 4.6 years ago by ▴ 10
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5
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697
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DESeq2 setting significant p-value
DESeq2
updated 6 days ago by 41k • written 5.0 years ago by ▴ 10
9
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 7 days ago by • 0 • written 8.8 years ago by ▴ 30
40 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?
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