Showing : DESeq2 • reset
6
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 days ago by • 0 • written 4.6 years ago by ▴ 10
0
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2
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1.5k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 9 days ago by • 0 • written 16 months ago by ▴ 10
1
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2
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747
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 23 days ago Patadù ▴ 10
1
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4
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531
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DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 18 days ago JKim • 0
0
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8
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507
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 5 days ago by ▴ 30 • written 6 days ago by • 0
0
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4
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449
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
2 days ago • updated 11 hours ago Ken C • 0
2
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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 24 days ago by 65k • written 24 days ago by • 0
2
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7
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396
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 days ago • updated 8 days ago sajadahmad41454 • 0
0
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8
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388
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 24 days ago by ★ 1.4k • written 26 days ago by • 0
1
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4
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360
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
25 days ago • updated 23 days ago winwater0928 • 0
3
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1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by 42k • written 26 days ago by ▴ 40
1
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3
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305
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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 11 days ago by ★ 4.1k • written 18 days ago by • 0
0
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3
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302
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
0
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6
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297
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 15 days ago by ★ 1.4k • written 17 days ago by ▴ 130
3
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3
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271
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 20 days ago by ★ 4.1k • written 21 days ago by ▴ 10
0
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4
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270
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 29 days ago lonn • 0
4
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9
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257
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
1
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3
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255
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 23 days ago by 42k • written 24 days ago by • 0
2
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3
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254
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 14 days ago by ★ 4.1k • written 16 days ago by • 0
3
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3
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253
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 26 days ago by 42k • written 27 days ago by • 0
1
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2
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247
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
6 days ago • updated 3 days ago BioinfGuru ▴ 30
1
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3
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237
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Different Shrunk Log2FC according with reference
DESeq2
updated 25 days ago by 42k • written 25 days ago by ▴ 20
0
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2
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229
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PCA plot suggestions
DESeq2 PCAtools
updated 23 days ago by 42k • written 25 days ago by • 0
0
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3
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225
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
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2
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214
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Deseq2 and Normalization of RNA sequencing data
DESeq2
18 days ago • updated 17 days ago kcarey • 0
1
vote
1
reply
193
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Handling multiple differential expression comparisons
DESeq2
updated 14 days ago by 42k • written 16 days ago by ▴ 10
0
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1
reply
173
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 9 days ago by ★ 4.1k • written 9 days ago by • 0
0
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2
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170
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 days ago • updated 16 days ago Aurora • 0
0
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2
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169
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DESeq2 v1.35.0
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
0
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1
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166
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 25 days ago by 42k • written 25 days ago by • 0
1
vote
1
reply
158
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
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1
reply
139
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
0
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1
reply
137
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putting my own expression data in deseq2
DESeq2
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
0
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3
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117
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 4 days ago by 42k • written 5 days ago by • 0
0
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2
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116
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 2 days ago by • 0
0
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1
reply
109
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
0
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1
reply
98
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 5 days ago by 42k • written 6 days ago by • 0
0
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0
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17
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LRT, more than two conditions and pairwise comparisons
DESeq2
10 hours ago boczniak767 ▴ 720
38 results • Page 1 of 1
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Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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