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
updated 1 hour ago by 65k • written 3 hours ago by • 0
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1
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37
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PCA plot suggestions
DESeq2 PCAtools
updated 1 hour ago by • 0 • written 12 hours ago by • 0
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3
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108
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 2 hours ago by 65k • written 1 day ago by • 0
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8
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224
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 hours ago by ★ 1.3k • written 2 days ago by • 0
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1
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 19 hours ago by 41k • written 22 hours ago by • 0
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3
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87
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Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 20
3
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1
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181
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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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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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157
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by 41k • written 2 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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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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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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5
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696
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DESeq2 setting significant p-value
DESeq2
updated 6 days ago by 41k • written 5.0 years ago by ▴ 10
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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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89
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rlog transformation
DESeq2
updated 7 days ago by 41k • written 7 days ago by • 0
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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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97
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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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113
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covariate with negative and positive values
DESeq2
updated 7 days ago by 41k • written 8 days ago by • 0
9
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12
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7.8k
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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
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1
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114
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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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5
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 days ago by • 0 • written 10 months ago by • 0
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4
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568
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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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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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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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193
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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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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 15 days ago by • 0
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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
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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
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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 21 days ago by • 0
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2
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153
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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
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
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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
1
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8
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1.2k
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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
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1
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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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2
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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
2
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3
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324
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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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7
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408
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
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159
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collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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2
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201
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
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2
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211
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
2
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3
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285
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 20
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3
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243
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Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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7
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679
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DESeq2 unable to handle large count values
DESeq2
updated 5 weeks ago by 41k • written 5 months ago by • 0
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1
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164
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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
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1
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132
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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1
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165
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
50 results • Page 1 of 1
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Replies
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…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
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?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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