Showing : DESeq2 • reset
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 7 hours ago by ★ 4.1k • written 7 hours ago by • 0
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118
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Handling multiple differential expression comparisons
DESeq2
updated 3 days ago by 42k • written 4 days ago by ▴ 10
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6
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228
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 4 days ago by ★ 1.3k • written 5 days ago by ▴ 130
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3
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186
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
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2
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115
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DESeq2 v1.35.0
DESeq2
updated 5 days ago by 42k • written 5 days ago by • 0
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2
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151
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Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago kcarey • 0
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3
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155
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
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3
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234
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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 7 hours ago by ★ 4.1k • written 6 days ago by • 0
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3
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260
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by 42k • written 7 days ago by • 0
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121
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
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2
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130
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
8 days ago • updated 5 days ago Aurora • 0
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1
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111
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
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114
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putting my own expression data in deseq2
DESeq2
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
3
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3
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241
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 9 days ago by ★ 4.1k • written 9 days ago by ▴ 10
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2
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214
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PCA plot suggestions
DESeq2 PCAtools
updated 12 days ago by 42k • written 13 days ago by • 0
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3
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227
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 12 days ago by 42k • written 12 days ago by • 0
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9
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396
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 13 days ago by • 0
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155
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 13 days ago by 42k • written 13 days ago by • 0
1
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3
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217
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Different Shrunk Log2FC according with reference
DESeq2
updated 14 days ago by 42k • written 14 days ago by ▴ 20
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4
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338
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
14 days ago • updated 12 days ago winwater0928 • 0
3
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1
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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 14 days ago by 42k • written 14 days ago by ▴ 40
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8
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356
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 13 days ago by ★ 1.3k • written 15 days ago by • 0
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3
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231
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
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139
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rlog transformation
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
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113
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 days ago by 42k • written 20 days ago by • 0
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2
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720
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
21 days ago • updated 12 days ago ussarizona ▴ 10
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1
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135
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covariate with negative and positive values
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
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1
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152
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
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4
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242
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
21 days ago • updated 18 days ago lonn • 0
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3
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209
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 22 days ago by 42k • written 23 days ago by ▴ 20
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245
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How to retrieve detailed regression results from deseq2
DESeq2
27 days ago • updated 18 days ago Weiqian ▴ 10
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4
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272
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DEG with low counts
DESeq2
updated 19 days ago by 42k • written 23 days ago by • 0
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133
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Deseq2 Rlog transformation
DESeq2
updated 23 days ago by ★ 4.1k • written 24 days ago by • 0
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2
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199
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Design Matrix within group comparison more than two groups
DESeq2
25 days ago hemantcnaik • 0
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137
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Bioinformatics student
Des DESeq2
updated 25 days ago by • 0 • written 26 days ago by • 0
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178
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DESeq2 gives an error and R crashes
DESeq2
27 days ago • updated 26 days ago Shefali • 0
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2
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223
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 28 days ago by 42k • written 4 weeks ago by ▴ 30
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1
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168
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 28 days ago by 42k • written 28 days ago by • 0
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2
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249
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Regressing out batch effects
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
0
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2
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173
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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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170
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DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
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6
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438
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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158
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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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174
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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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268
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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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1
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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 5 weeks ago by 42k • written 5 weeks ago by • 0
2
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3
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359
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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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171
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collapseReplicates dimension error
DESeq2 Dese
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
3
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2
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220
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
6 weeks ago Anita ▴ 10
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2
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239
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago Chanderkant Chaudhary • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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