Showing : DESEQ2 • reset
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Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by 42k • written 4 days ago by ▴ 10
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3
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182
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 4 days ago by • 0
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6
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220
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 3 days ago by ★ 1.3k • written 5 days ago by ▴ 130
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2
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128
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
7 days ago • updated 4 days ago Aurora • 0
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2
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147
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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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2
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112
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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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3
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150
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
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3
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256
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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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1
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154
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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 6 days ago by ★ 4.1k • written 6 days ago by • 0
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4
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483
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 6 days ago JKim • 0
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19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 7 days ago by • 0 • written 4.6 years ago by ▴ 10
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116
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
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1
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109
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by 42k • written 8 days ago by • 0
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1
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113
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putting my own expression data in deseq2
DESeq2
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
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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 8 days ago by ★ 4.1k • written 8 days ago by ▴ 10
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2
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214
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PCA plot suggestions
DESeq2 PCAtools
updated 11 days ago by 42k • written 12 days ago by • 0
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717
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago ussarizona ▴ 10
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3
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227
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 11 days ago by 42k • written 12 days ago by • 0
1
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4
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335
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago winwater0928 • 0
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9
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393
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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 12 days ago by • 0
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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 12 days ago by ★ 1.3k • written 14 days ago by • 0
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1
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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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216
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Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by 42k • written 13 days ago by ▴ 20
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 13 days ago by 42k • written 14 days ago by ▴ 40
3
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3
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231
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by 42k • written 15 days ago by • 0
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4
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240
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 days ago • updated 17 days ago lonn • 0
1
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2
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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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7
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424
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DESeq filtering specific to contrasts
DESeq2
updated 18 days ago by 42k • written 11 weeks ago by • 0
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5
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757
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DESeq2 setting significant p-value
DESeq2
updated 18 days ago by 42k • written 5.0 years ago by ▴ 10
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4
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270
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DEG with low counts
DESeq2
updated 18 days ago by 42k • written 23 days ago by • 0
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1
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139
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rlog transformation
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
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1
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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 19 days ago by • 0
0
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1
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135
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covariate with negative and positive values
DESeq2
updated 19 days ago by 42k • written 21 days ago by • 0
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 19 days ago by • 0 • written 8.8 years ago by ▴ 30
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1
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150
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
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4
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603
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 days ago by 42k • written 6 months ago by • 0
0
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3
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207
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 20
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1
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133
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Deseq2 Rlog transformation
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
1
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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 • updated 24 days ago hemantcnaik • 0
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1
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137
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Bioinformatics student
Des DESeq2
updated 25 days ago by • 0 • written 25 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 27 days ago by 42k • written 4 weeks ago by ▴ 30
0
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1
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167
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 27 days ago by 42k • written 28 days ago by • 0
0
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2
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249
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Regressing out batch effects
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
0
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2
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172
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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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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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437
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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
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 • updated 4 weeks ago michelafrancesconi8 • 0
1
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1
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158
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago • updated 4 weeks ago Layal • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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Popular Question to Gyan Prakash Mishra ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
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