Showing : Deseq2 • reset
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 53 minutes ago by ★ 4.1k • written 59 minutes ago by • 0
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44
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 23 hours ago by ★ 4.1k • written 1 day ago by • 0
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5
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148
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
2 days ago • updated 5 hours ago sajadahmad41454 • 0
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203
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 4 days ago by ★ 4.1k • written 6 days ago by • 0
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137
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Handling multiple differential expression comparisons
DESeq2
updated 4 days ago by 42k • written 6 days ago by ▴ 10
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242
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 days ago by ★ 1.4k • written 7 days ago by ▴ 130
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125
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DESeq2 v1.35.0
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
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163
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Deseq2 and Normalization of RNA sequencing data
DESeq2
8 days ago • updated 7 days ago kcarey • 0
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 days ago by ★ 4.1k • written 8 days ago by • 0
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257
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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 2 days ago by ★ 4.1k • written 8 days ago by • 0
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266
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 days ago by 42k • written 9 days ago by • 0
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131
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 9 days ago by 42k • written 9 days ago by • 0
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121
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putting my own expression data in deseq2
DESeq2
updated 9 days ago by ★ 4.1k • written 10 days ago by • 0
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142
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
10 days ago • updated 7 days ago Aurora • 0
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120
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 11 days ago by ★ 4.1k • written 11 days ago by ▴ 10
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234
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 13 days ago by 42k • written 14 days ago by • 0
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 14 days ago by 65k • written 14 days ago by • 0
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215
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PCA plot suggestions
DESeq2 PCAtools
updated 13 days ago by 42k • written 15 days ago by • 0
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156
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 15 days ago by 42k • written 15 days ago by • 0
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222
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Different Shrunk Log2FC according with reference
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 20
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343
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago winwater0928 • 0
3
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316
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by 42k • written 16 days ago by ▴ 40
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 15 days ago by ★ 1.4k • written 16 days ago by • 0
3
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3
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234
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
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142
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rlog transformation
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
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115
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 days ago by 42k • written 22 days ago by • 0
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4
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246
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
22 days ago • updated 20 days ago lonn • 0
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721
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
22 days ago • updated 13 days ago ussarizona ▴ 10
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153
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
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135
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covariate with negative and positive values
DESeq2
updated 21 days ago by 42k • written 23 days ago by • 0
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3
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209
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 20
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4
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277
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DEG with low counts
DESeq2
updated 20 days ago by 42k • written 25 days ago by • 0
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135
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Deseq2 Rlog transformation
DESeq2
updated 24 days ago by ★ 4.1k • written 26 days ago by • 0
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200
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Design Matrix within group comparison more than two groups
DESeq2
27 days ago • updated 26 days ago hemantcnaik • 0
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137
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Bioinformatics student
Des DESeq2
updated 27 days ago by • 0 • written 27 days ago by • 0
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180
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DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago Shefali • 0
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246
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How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago Weiqian ▴ 10
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173
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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174
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
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228
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 30
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252
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Regressing out batch effects
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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172
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DESeq2 - Missing values in count matrix
DESeq2
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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6
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447
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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161
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago Layal • 0
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2
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175
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago michelafrancesconi8 • 0
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4
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273
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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168
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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361
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PCA of different bacterial species
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 10
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222
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
6 weeks ago Anita ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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