Showing : DESeq2 • reset
6
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19
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2.6k
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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
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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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745
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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
vote
4
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531
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DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 17 days ago JKim • 0
0
votes
8
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502
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 4 days ago by ▴ 30 • written 5 days ago by • 0
2
votes
9
replies
427
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 23 days ago by 65k • written 24 days ago by • 0
0
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8
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387
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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
2
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7
replies
386
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 days ago • updated 8 days ago sajadahmad41454 • 0
0
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4
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361
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
2 days ago • updated 11 minutes ago Ken C • 0
1
vote
4
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359
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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
328
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 25 days ago by 42k • written 25 days ago by ▴ 40
1
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3
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304
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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 17 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 17 days ago by 42k • written 18 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 16 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 20 days ago by ▴ 10
0
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4
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269
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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
1
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2
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265
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 29 days ago Weiqian ▴ 10
1
vote
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 23 days ago by • 0
2
votes
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 15 days ago by • 0
4
votes
9
replies
252
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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
3
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3
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252
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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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243
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
5 days ago • updated 2 days ago BioinfGuru ▴ 30
1
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3
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236
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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 24 days ago by • 0
0
votes
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 17 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
17 days ago • updated 16 days ago kcarey • 0
1
vote
1
reply
192
views
Handling multiple differential expression comparisons
DESeq2
updated 14 days ago by 42k • written 15 days ago by ▴ 10
0
votes
1
reply
170
views
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
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 days ago • updated 16 days ago Aurora • 0
0
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1
reply
165
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 24 days ago by 42k • written 25 days ago by • 0
0
votes
2
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165
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
1
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1
reply
157
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 19 days ago by • 0
0
votes
1
reply
137
views
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
replies
113
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 4 days ago by 42k • written 4 days ago by • 0
0
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2
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111
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 2 days ago by • 0
0
votes
1
reply
108
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
0
votes
1
reply
94
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 5 days ago by 42k • written 6 days ago by • 0
38 results • Page 1 of 1
Recent ...
Replies
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…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
Thank you for advice, you mean I need to add: countdata_rat <- data.frame(condition = as.factor(METADATA_RAT$treatment)) and total: dds_…
Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
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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