Showing : DESeq2 • reset
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Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2 limma
updated 2 hours ago by ★ 1.1k • written 1 day ago by ▴ 20
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44
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Removing Ig* and H2-* genes and counts from txi after DESeqDataSetFromTximport() in a DESeq2 analysis prior to DESeq() and results()?
DESeq2 tximport
3 days ago Pratik Mehta ▴ 10
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48
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Comparing different method for DESEQ2
DESeq2 GeneExpression
3 days ago Vapin • 0
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43
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Time serious analysis Wald test in results()
DESeq2 TimeSeriesExperiment
4 days ago Jason • 0
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0
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74
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DESEQ2 time series with multiple variables
DESeq2
4 days ago Abel • 0
0
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4
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113
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Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2 log2FC
5 days ago User000 • 0
2
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4
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174
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DESEQ2 several samples per individual
DESeq2
6 days ago • updated 5 days ago Bine ▴ 20
0
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1
reply
105
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Comparison between treatment timepoints in a single timeseries (control is first timepoint)
DESeq2 single-timeseries TimeSeriesExperiment
updated 6 days ago by 38k • written 13 days ago by • 0
0
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1
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73
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 6 days ago by 38k • written 9 days ago by ▴ 10
1
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1
reply
113
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Contrasts in Deseq2
DESeq2
updated 6 days ago by 38k • written 10 days ago by • 0
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3
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178
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
8 days ago • updated 5 days ago marinaw • 0
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1
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91
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interaction term formula for DESEQ2?
DESeq2
updated 7 days ago by ★ 1.1k • written 7 days ago by • 0
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1
reply
114
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Bioconductor Rpackages install
DESeq2
updated 8 days ago by ★ 1.6k • written 8 days ago by • 0
1
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2
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95
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Do we need to correct any of the data from DESeq2, if we only want to investigate some of the comparisons?
DESeq2 correction
10 days ago • updated 6 days ago smac97 • 0
0
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3
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124
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Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 11 days ago by 61k • written 12 days ago by • 0
2
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2
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143
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Gene abundance DESEq
DESeq2
updated 12 days ago by ★ 1.6k • written 13 days ago by • 0
1
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3
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128
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Clarification about DESeq2 counts() function when dealing with covariates
DESeq2
updated 12 days ago by ★ 1.1k • written 12 days ago by • 0
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5
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131
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DESeq2 is not available for R version 4.2.1
DESeq2
13 days ago annamariabugaj ▴ 10
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2
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66
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Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 13 days ago by • 0 • written 13 days ago by • 0
1
vote
2
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123
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DESEQ2 Normalisation Factor
DESeq2
16 days ago • updated 15 days ago MAHESH • 0
0
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1
reply
74
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DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 16 days ago by 38k • written 18 days ago by • 0
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5
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207
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Weird looking volcano plot
DESeq2 volcano
19 days ago • updated 6 days ago nico • 0
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1
reply
114
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 16 days ago by 38k • written 23 days ago by • 0
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2
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122
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DESeq2 with incorrect adjusted Pvalues
DESeq2
updated 16 days ago by 38k • written 17 days ago by • 0
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2
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133
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Overwhelmed by DESEq2 options and how to answer my questions.: Two conditions and Three families
DESeq2
18 days ago • updated 17 days ago lgspeight • 0
1
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3
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135
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different stat and p values when filtering or not by lfc in DESeq2
DESeq2 wald stat
updated 18 days ago by ▴ 610 • written 19 days ago by • 0
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3
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104
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code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 16 days ago by 38k • written 20 days ago by • -60
1
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1
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66
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What is the effect of passage number in the differential gene expression when performing RNA sequencing analysis?
DESeq2 passagenumber
updated 20 days ago by ★ 1.6k • written 21 days ago by • 0
1
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1
reply
86
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 20 days ago by ★ 1.6k • written 20 days ago by • 0
0
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2
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115
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clarification of the way of converting standard error to confidence interval for logFC in DESeq2 result table
DESeq2 Confidence.Interval
22 days ago • updated 21 days ago Mike • -60
0
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1
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120
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ref treatment
DESeq2
updated 20 days ago by ★ 1.1k • written 21 days ago by • 0
1
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1
reply
103
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Time-series analyses of a multifactor design with DESeq2
DESeq2 MultipleFactors TimeSeriesExperiment
updated 24 days ago by 38k • written 26 days ago by • 0
0
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4
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169
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DESeq2 lfcThreshold - all my padj are equal to 1
DESeq2 lfcThreshold
24 days ago • updated 14 days ago a.khazaal • 0
1
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2
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151
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 25 days ago by ★ 1.1k • written 25 days ago by • 0
5
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6
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282
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Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 15 days ago by 46k • written 26 days ago by • 0
0
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2
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122
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output file conversion from FeatureCount to DESeq2 - no duplicate for samples
DESeq2 FeatureCount
updated 26 days ago by ★ 1.6k • written 26 days ago by • 0
2
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3
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195
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DESeq2 contrasts using all relevant samples vs all samples
DESeq2
27 days ago • updated 25 days ago jeffrey.maurer • 0
0
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7
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225
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DESeq2 Error in checkContrast(contrast, resNames) : when using list()
DESeq2
updated 26 days ago by 38k • written 27 days ago by ▴ 10
4
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1
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130
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Log2FC values slightly higher in some genes after DESeq2 shrinkage
DESeq2
updated 27 days ago by 38k • written 28 days ago by ▴ 10
1
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3
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144
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resultsNames(dds) not showing all contrasts
DESeq2 resultsNames lfcShrink
updated 28 days ago by ★ 1.6k • written 4 weeks ago by • 0
1
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5
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293
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DESeq2 - Replacing outliers with continuous variable in design
DESeq2
updated 26 days ago by 38k • written 5 weeks ago by • 0
0
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1
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93
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 4 weeks ago by 38k • written 4 weeks ago by • 0
0
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3
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229
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Time course RNA seq with DESeq2
DESeq2
updated 4 weeks ago by ▴ 10 • written 5 weeks ago by • 0
0
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1
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115
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DESeq2 analysis with 3 factors
DESeq2
updated 4 weeks ago by 38k • written 4 weeks ago by ▴ 10
0
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1
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137
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How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 4 weeks ago by 38k • written 4 weeks ago by ▴ 20
0
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1
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121
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DESeq2 Design Matrix
DESeq2
updated 4 weeks ago by 38k • written 4 weeks ago by ▴ 10
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4
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185
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DESeq2 likehood ratio
DESeq2
updated 27 days ago by 38k • written 5 weeks ago by • 0
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1
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103
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DESeq2 likehood ratio
DESeq2
updated 4 weeks ago by 38k • written 4 weeks ago by • 0
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1
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146
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 4 weeks ago by 38k • written 5 weeks ago by • 0
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3
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169
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DESEq2 rerun gives different results
DESeq2
4 weeks ago Mia • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: CountOverlap by James W. MacDonald 61k
When you `suppressWarnings` you won't get warnings that tell you that there are problems! The main warning you will be suppressing will loo…
Comment: Different results between Limma and DESEQ2 for Differential Expression Analysis by swbarnes2 ★ 1.1k
You are using two different algorithms. You should expect them to be close, but you can't expect them to be identical.
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by JoAMWil • 0
Hi Michael, Thank you for the answers above. What might you suggest for a RIP-seq experiment with three assays - IP, input and IgG non-sp…
Comment: Question on performing filtering by gene expression on a normalized matrix in li by mohammedtoufiq91 ▴ 10
@gordonsmyth thank you for your response.
Comment: Different results between Limma and DESEQ2 for Differential Expression Analysis by Bine ▴ 20
Thank you. Sorry I think I am a bit confused. I agree I should be more clear and show the complete analysis. **Input Limma & DESEQ2:** …
Votes
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: Problem loading R packages on MacBook Pro
Comment: Question on performing filtering by gene expression on a normalized matrix in li
Answer: Different results between Limma and DESEQ2 for Differential Expression Analysis
Answer: Different results between Limma and DESEQ2 for Differential Expression Analysis
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