Showing : desEQ2 • reset
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 2 hours ago by 42k • written 1 day ago by • 0
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68
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 2 hours ago by 42k • written 1 day ago by • 0
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9
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241
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
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3
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106
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 3 days ago by 42k • written 3 days ago by • 0
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 4 days ago by 42k • written 5 days ago by • 0
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 3 days ago by ▴ 30 • written 4 days ago by • 0
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
4 days ago • updated 1 day ago BioinfGuru ▴ 30
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
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101
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 9 days ago by ★ 4.1k • written 9 days ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 days ago • updated 7 days ago sajadahmad41454 • 0
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Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by 42k • written 14 days ago by ▴ 10
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 14 days ago by ★ 1.4k • written 15 days ago by ▴ 130
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
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DESeq2 v1.35.0
DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
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Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago kcarey • 0
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
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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 10 days ago by ★ 4.1k • written 16 days ago by • 0
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
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156
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
18 days ago • updated 15 days ago Aurora • 0
0
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138
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
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135
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putting my own expression data in deseq2
DESeq2
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 days ago by ★ 4.1k • written 19 days ago by ▴ 10
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PCA plot suggestions
DESeq2 PCAtools
updated 22 days ago by 42k • written 23 days ago by • 0
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253
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 22 days ago by 42k • written 22 days ago by • 0
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9
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427
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 23 days ago by • 0
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165
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 23 days ago by 42k • written 23 days ago by • 0
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Different Shrunk Log2FC according with reference
DESeq2
updated 24 days ago by 42k • written 24 days ago by ▴ 20
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356
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago winwater0928 • 0
3
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328
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by 42k • written 24 days ago by ▴ 40
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 23 days ago by ★ 1.4k • written 25 days ago by • 0
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
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158
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rlog transformation
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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740
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 22 days ago Patadù ▴ 10
0
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149
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covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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167
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
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265
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 28 days ago lonn • 0
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3
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230
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
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262
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago Weiqian ▴ 10
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292
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DEG with low counts
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
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145
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Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
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211
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Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
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149
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Bioinformatics student
Des DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
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196
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DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
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2
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245
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
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187
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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265
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Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
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182
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
1
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1
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188
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DESeq2 - Missing values in count matrix
DESeq2
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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