Showing : Deseq2 • reset
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
16 hours ago • updated 15 hours ago shaunpeterson • 0
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127
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 3 hours ago by • 0 • written 22 hours ago by • 0
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232
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
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3
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104
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 2 days ago by 42k • written 3 days ago by • 0
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226
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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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8
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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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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 3 days ago by 42k • written 4 days ago by • 0
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161
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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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100
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 days ago • updated 6 days ago sajadahmad41454 • 0
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
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185
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Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by 42k • written 14 days ago by ▴ 10
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6
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291
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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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DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
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209
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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 15 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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3
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300
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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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155
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
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135
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putting my own expression data in deseq2
DESeq2
updated 17 days ago by ★ 4.1k • written 17 days ago by • 0
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166
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
18 days ago • updated 14 days ago Aurora • 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 17 days ago by 42k • 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 18 days ago by ★ 4.1k • written 19 days ago by ▴ 10
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253
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
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9
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426
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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 22 days ago by • 0
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2
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226
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PCA plot suggestions
DESeq2 PCAtools
updated 21 days ago by 42k • 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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235
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Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 20
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4
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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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8
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 23 days ago by ★ 1.4k • written 24 days ago by • 0
3
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3
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250
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
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157
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rlog transformation
DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
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124
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 29 days ago by 42k • written 29 days ago by • 0
0
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4
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263
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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
1
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2
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738
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago Patadù ▴ 10
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166
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by ★ 4.1k • written 4 weeks ago by • 0
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149
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covariate with negative and positive values
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
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3
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229
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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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4
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292
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DEG with low counts
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
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144
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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 • updated 4 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
1
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2
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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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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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2
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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
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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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2
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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
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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Replies
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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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