Showing : DESeq2 • reset
9
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6 days ago by • 0 • written 8.8 years ago by ▴ 30
6
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16
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2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by 41k • written 4.6 years ago by ▴ 10
3
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3
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146
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
2
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3
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324
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PCA of different bacterial species
DESeq2
updated 28 days ago by 41k • written 29 days ago by ▴ 10
2
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5
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694
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DESeq2 setting significant p-value
DESeq2
updated 5 days ago by 41k • written 5.0 years 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 7 days ago by • 0 • written 10 months ago by • 0
2
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1
reply
153
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 hours ago by 41k • written 1 day ago by ▴ 40
1
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3
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74
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Different Shrunk Log2FC according with reference
DESeq2
updated 12 hours ago by 41k • written 17 hours ago by ▴ 20
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2
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163
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Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago hemantcnaik • 0
1
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2
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217
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How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
1
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1
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135
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago Layal • 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
1
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6
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401
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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
1
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1
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 days ago by • 0
1
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2
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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
0
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2
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219
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Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
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4
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229
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DEG with low counts
DESeq2
updated 5 days ago by 41k • written 10 days ago by • 0
0
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1
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109
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Deseq2 Rlog transformation
DESeq2
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
0
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4
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564
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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
0
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2
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142
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
0
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1
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59
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 8 hours ago by ★ 1.3k • written 17 hours ago by • 0
0
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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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4
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121
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 8 hours ago by ★ 1.3k • written 1 day ago by • 0
0
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1
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53
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 hours ago by 41k • written 8 hours ago by • 0
0
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7
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406
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
0
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1
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117
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Bioinformatics student
Des DESeq2
updated 12 days ago by • 0 • written 12 days ago by • 0
0
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3
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173
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
0
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1
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137
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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
0
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4
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229
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
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2
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151
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
22 days ago • updated 21 days ago michelafrancesconi8 • 0
0
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2
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192
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 19 days ago by ▴ 30
0
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7
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384
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DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by 41k • written 9 weeks ago by • 0
0
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1
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110
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covariate with negative and positive values
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
0
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1
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154
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DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
0
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1
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112
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by ★ 4.0k • written 7 days ago by • 0
0
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4
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191
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
0
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1
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95
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
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1
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85
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 6 days ago by • 0
0
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1
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87
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rlog transformation
DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
0
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1
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157
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collapseReplicates dimension error
DESeq2 Dese
updated 29 days ago by 41k • written 4 weeks ago by • 0
40 results • Page 1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
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A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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