Showing : deseq2 • reset
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Once again a "Model matrix not full rank"
DESeq2 design coldata
14 hours ago • updated 5 hours ago arfranco ▴ 130
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2
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55
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DESeq2 v1.35.0
DESeq2
updated 18 hours ago by 41k • written 19 hours ago by • 0
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2
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81
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Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 12 hours ago kcarey • 0
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3
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97
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
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1
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105
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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 1 day ago by ★ 4.1k • written 1 day ago by • 0
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3
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221
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
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1
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85
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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2
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88
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 1 hour ago Aurora • 0
0
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1
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88
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
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1
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88
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putting my own expression data in deseq2
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
3
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3
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199
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 4 days ago by ★ 4.1k • written 4 days ago by ▴ 10
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2
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185
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PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 8 days ago by • 0
1
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3
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190
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
2
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9
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346
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 days ago by 65k • written 7 days ago by • 0
0
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1
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137
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
1
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3
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204
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Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
1
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4
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306
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago winwater0928 • 0
3
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1
reply
300
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 40
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8
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326
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 8 days ago by ★ 1.3k • written 9 days ago by • 0
3
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3
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213
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
0
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1
reply
127
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rlog transformation
DESeq2
updated 14 days ago by 41k • written 15 days ago by • 0
0
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1
reply
106
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 15 days ago by • 0
1
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2
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696
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
0
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1
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128
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covariate with negative and positive values
DESeq2
updated 14 days ago by 41k • written 16 days ago by • 0
0
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1
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139
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
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4
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230
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 13 days ago lonn • 0
0
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3
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200
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
1
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2
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239
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How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago Weiqian ▴ 10
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4
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260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
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1
reply
128
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Deseq2 Rlog transformation
DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
1
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2
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190
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Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
0
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1
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130
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Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
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1
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173
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DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago Shefali • 0
0
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2
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215
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 23 days ago by 41k • written 27 days ago by ▴ 30
0
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1
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159
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 23 days ago by 41k • written 23 days ago by • 0
0
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2
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234
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Regressing out batch effects
DESeq2
updated 23 days ago by 41k • written 28 days ago by • 0
0
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2
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161
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
1
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1
reply
160
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DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by 65k • written 28 days ago by • 0
1
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6
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419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 29 days ago by 41k • written 29 days ago by • 0
1
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1
reply
150
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
0
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2
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168
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
0
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4
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254
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
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1
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159
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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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346
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PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
0
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1
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169
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collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
3
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2
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211
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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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229
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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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226
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
2
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3
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302
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by ▴ 20
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3
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260
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Help with Complex DESeq2 Design
DESeq2
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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