Showing : DESeq2 • reset
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Once again a "Model matrix not full rank"
DESeq2 design coldata
20 minutes ago • updated just now arfranco ▴ 130
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DESeq2 v1.35.0
DESeq2
updated 4 hours ago by 41k • written 5 hours ago by • 0
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3
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91
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 10 hours ago by ★ 4.1k • written 22 hours ago by • 0
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1
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48
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Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 11 hours ago by ★ 4.1k • written 22 hours ago by • 0
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3
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213
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
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94
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
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4
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452
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
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2.4k
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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 • 0 • written 4.6 years ago by ▴ 10
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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1
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74
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
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1
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85
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
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1
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82
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putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
3
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3
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195
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
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2
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181
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PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
1
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2
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694
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
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4
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299
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
2
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9
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341
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 days ago by 65k • written 7 days ago by • 0
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8
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323
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 days ago by ★ 1.3k • written 9 days ago by • 0
0
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1
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130
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
1
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3
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201
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Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 20
3
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1
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295
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 40
3
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3
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213
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
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4
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229
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 12 days ago lonn • 0
1
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2
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237
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How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 13 days ago Weiqian ▴ 10
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7
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403
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DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by 41k • written 11 weeks ago by • 0
2
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5
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734
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DESeq2 setting significant p-value
DESeq2
updated 13 days ago by 41k • written 5.0 years ago by ▴ 10
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4
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260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
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1
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123
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rlog transformation
DESeq2
updated 14 days ago by 41k • written 14 days ago by • 0
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1
reply
105
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 14 days ago by • 0
0
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1
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128
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covariate with negative and positive values
DESeq2
updated 14 days ago by 41k • written 15 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 14 days ago by • 0 • written 8.8 years ago by ▴ 30
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1
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138
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
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4
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592
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
0
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3
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200
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
0
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1
reply
128
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Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
1
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2
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188
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Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
0
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1
reply
130
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Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
0
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1
reply
173
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DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
0
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2
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214
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 days ago by 41k • written 27 days ago by ▴ 30
0
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1
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157
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 22 days ago by 41k • written 23 days ago by • 0
0
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2
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233
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Regressing out batch effects
DESeq2
updated 22 days ago by 41k • written 28 days ago by • 0
0
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2
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159
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
1
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1
reply
160
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DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by 65k • written 28 days ago by • 0
1
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6
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419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 29 days ago by • 0
0
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2
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166
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago • updated 29 days ago michelafrancesconi8 • 0
1
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1
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149
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago Layal • 0
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4
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252
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks 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 4 weeks ago by ★ 13k • written 10 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank" by James W. MacDonald 65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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