Showing : DESEQ2 • reset
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Handling multiple differential expression comparisons
DESeq2
updated 15 hours ago by 41k • written 2 days ago by ▴ 10
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6
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190
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 3 days ago by ▴ 130
2
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3
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150
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 hours ago by ★ 4.1k • written 2 days ago by • 0
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2
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93
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
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2
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127
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Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago kcarey • 0
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3
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131
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
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1
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132
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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 4 days ago by ★ 4.1k • written 4 days ago by • 0
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3
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242
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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103
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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2
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119
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
5 days ago • updated 2 days ago Aurora • 0
0
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1
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100
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
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1
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101
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putting my own expression data in deseq2
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
3
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3
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223
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
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2
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205
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PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 10 days ago by • 0
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3
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214
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 10 days ago by • 0
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9
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388
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 10 days ago by • 0
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1
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152
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 11 days ago by • 0
1
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3
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210
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Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
1
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4
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323
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago winwater0928 • 0
3
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1
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309
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 40
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8
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343
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 days ago by ★ 1.3k • written 12 days ago by • 0
3
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3
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227
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by 41k • written 13 days ago by • 0
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1
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136
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rlog transformation
DESeq2
updated 17 days ago by 41k • written 17 days ago by • 0
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1
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112
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 days ago by 41k • written 17 days ago by • 0
1
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2
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710
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago ussarizona ▴ 10
0
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1
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133
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covariate with negative and positive values
DESeq2
updated 17 days ago by 41k • written 19 days ago by • 0
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1
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148
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
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4
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236
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
0
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3
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204
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by 41k • written 20 days ago by ▴ 20
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2
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241
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How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago Weiqian ▴ 10
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4
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269
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DEG with low counts
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
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1
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130
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Deseq2 Rlog transformation
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
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2
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193
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Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago hemantcnaik • 0
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1
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132
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Bioinformatics student
Des DESeq2
updated 23 days ago by • 0 • written 23 days ago by • 0
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175
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DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago Shefali • 0
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2
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220
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 26 days ago by 41k • written 4 weeks ago by ▴ 30
0
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1
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162
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 26 days ago by 41k • written 26 days ago by • 0
0
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2
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247
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Regressing out batch effects
DESeq2
updated 26 days ago by 41k • written 4 weeks ago by • 0
0
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2
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171
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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
1
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1
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167
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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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433
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
1
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1
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156
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
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2
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173
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
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4
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261
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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1
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160
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
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3
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351
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PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
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1
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170
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collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
3
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2
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215
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
1
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2
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234
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
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2
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229
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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