Showing : DEseq2 • reset
5
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 6 hours ago by • 0 • written 4.6 years ago by ▴ 10
9
votes
12
replies
7.7k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 1 day ago by • 0 • written 8.8 years ago by ▴ 30
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 19 days ago by ★ 13k • written 9 months ago by ▴ 10
0
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7
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397
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 24 days ago fr8712ca-s • 0
0
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7
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334
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DESeq filtering specific to contrasts
DESeq2
updated 6 hours ago by 41k • written 9 weeks ago by • 0
1
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6
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392
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 15 days ago by 41k • written 16 days ago by • 0
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 2 days ago by • 0 • written 10 months ago by • 0
2
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5
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661
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DESeq2 setting significant p-value
DESeq2
updated 7 hours ago by 41k • written 5.0 years ago by ▴ 10
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4
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216
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by 41k • written 17 days ago by • 0
0
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4
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198
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DEG with low counts
DESeq2
updated 10 hours ago by 41k • written 5 days ago by • 0
0
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4
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554
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 3 days ago by 41k • written 5 months ago by • 0
0
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3
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142
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by 41k • written 4 days ago by ▴ 20
0
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3
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108
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
updated 14 hours ago by ★ 4.0k • written 2 days ago by • 0
2
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3
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274
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by ▴ 20
2
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3
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314
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PCA of different bacterial species
DESeq2
updated 23 days ago by 41k • written 24 days ago by ▴ 10
0
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2
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198
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago • updated 29 days ago kcarey • 0
0
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2
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215
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Regressing out batch effects
DESeq2
updated 9 days ago by 41k • written 15 days ago by • 0
1
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2
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198
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
29 days ago • updated 23 days ago Chanderkant Chaudhary • 0
3
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2
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190
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
25 days ago Anita ▴ 10
0
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2
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132
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 14 days ago by 65k • written 14 days ago by • 0
1
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2
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156
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago hemantcnaik • 0
0
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2
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142
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 days ago • updated 16 days ago michelafrancesconi8 • 0
0
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2
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180
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 9 days ago by 41k • written 14 days ago by ▴ 30
1
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2
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179
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How to retrieve detailed regression results from deseq2
DESeq2
8 days ago • updated 2 hours ago Weiqian ▴ 10
0
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1
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134
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by 41k • written 22 days ago by • 0
0
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1
reply
49
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 1 day ago by 41k • written 1 day ago by • 0
0
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1
reply
110
views
Bioinformatics student
Des DESeq2
updated 7 days ago by • 0 • written 7 days ago by • 0
0
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1
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58
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
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76
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by ★ 4.0k • written 2 days ago by • 0
1
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1
reply
148
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DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by 65k • written 15 days ago by • 0
0
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1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by ★ 4.0k • written 5 days ago by • 0
0
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1
reply
130
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 9 days ago by 41k • written 10 days ago by • 0
0
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1
reply
142
views
DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago Shefali • 0
0
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1
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76
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covariate with negative and positive values
DESeq2
updated 1 day ago by 41k • written 3 days ago by • 0
0
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1
reply
148
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collapseReplicates dimension error
DESeq2 Dese
updated 24 days ago by 41k • written 28 days ago by • 0
0
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1
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53
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rlog transformation
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
1
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1
reply
129
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
17 days ago • updated 16 days ago Layal • 0
37 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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