Showing : DESeq2 • reset
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
15 days ago • updated 1 day ago jbnrodriguez • 0
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1
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136
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 6 days ago by 34k • written 6 days ago by • 0
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1
reply
109
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Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
updated 6 days ago by 34k • written 6 days ago by ▴ 10
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1
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58
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Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 6 days ago by 58k • written 6 days ago by • 0
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1
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100
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Log fold change interpretation of time series with Wald test
DESeq2
updated 7 days ago by ▴ 840 • written 7 days ago by • 0
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1
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124
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RNA Seq - Venn Diagramm - display exclusively expressed genes
VennDetail DESeq2
updated 7 days ago by 34k • written 7 days ago by • 0
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7
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237
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small dimensions in the matrix of counts from smallRNA using DESEq2
matrix DESeq2 SmallRNA dimensions small
8 days ago andreia • 0
1
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3
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165
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Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 8 days ago by 34k • written 10 days ago by ▴ 20
3
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2
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138
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Sequencing depth before and aftr normalisation with DESEQ2 doesn't look as expected: Problem?
normalisation DESEQ2
updated 9 days ago by ▴ 840 • written 9 days ago by • 0
3
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7
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330
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Nanostringdiff - defining contrast values for blocking variables in glm
limma edgeR DESeq2 NanoStringDiff
updated 6 days ago by 58k • written 13 days ago by • 0
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62
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error: cannot execute 'f951': execvp: No such file or directory when downloading DESeq2 package
DESeq2
15 days ago Yihan • 0
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3
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113
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 15 days ago by 34k • written 16 days ago by • 0
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1
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69
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What does one-sided p-value in DESeq2 mean in biological terms?
one-sided nbinomWaldTest p-value meta-analysis DESeq2
updated 16 days ago by 34k • written 17 days ago by • 0
1
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6
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192
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DESeq2 design for paired samples
DESeq2 paired
updated 15 days ago by 34k • written 16 days ago by ▴ 10
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1
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84
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Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 17 days ago by ▴ 20 • written 17 days ago by • 0
1
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4
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110
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normalising Biological replicates for differential analysis
DESeq2 Rtudio
updated 17 days ago by ▴ 840 • written 17 days ago by • 0
5
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6
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207
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How to calculate dispersion DESeq2 - Step by Step
DGE DESeq2 Differential
22 days ago • updated 17 days ago Zeke Smith ▴ 10
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1
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68
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pairwise within sample
DESeq2 microbiome
updated 19 days ago by 34k • written 20 days ago by • 0
2
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8
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361
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How does the design formula affect dispersion estimate in DESeq2?
deseq2
updated 19 days ago by 34k • written 12 months ago by • 0
0
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3
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127
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Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 19 days ago by 34k • written 21 days ago by • 0
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5
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210
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Recalculated abundance data output table with DEseq2
DESeq2
updated 10 hours ago by 34k • written 21 days ago by • 0
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2
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148
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log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
22 days ago • updated 20 days ago Claire • 0
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4
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388
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Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 3.5 years ago by • 0
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3
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120
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 18 days ago by 34k • written 22 days ago by • 0
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4
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144
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
22 days ago • updated 17 days ago khaveh ▴ 10
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1
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77
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Question about my design
DESeq2
updated 21 days ago by 34k • written 21 days ago by • 0
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1
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85
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 21 days ago by ▴ 830 • written 23 days ago by • 0
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7
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215
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DESEQ2 log2FC is not following Normalized read count
DESeq2
updated 18 days ago by 34k • written 24 days ago by • 0
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3
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169
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DESEQ PCA
DESeq2 miRNA
updated 24 days ago by ▴ 840 • written 28 days ago by • 0
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3
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118
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 15 days ago by 34k • written 25 days ago by • 0
5
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4
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138
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ylim and xlim in Enhanced Volcano
DESeq2 EnhancedVolcano Bioconductor
updated 26 days ago by 3.4k • written 26 days ago by • 0
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1
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136
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 28 days ago by 34k • written 28 days ago by • 0
0
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1
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167
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How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions
DESeq2
updated 28 days ago by 34k • written 28 days ago by • 0
1
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113
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pairwise comparison + interaction term in DESeq2
DESeq2 interaction pairwise
4 weeks ago Lucas • 0
1
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4
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232
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weird MAplot or volcano plot of DESeq2 diff result
DESeq2
updated 4 weeks ago by 34k • written 4 weeks ago by ▴ 20
1
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5
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198
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lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 18 days ago by 34k • written 4 weeks ago by ▴ 20
4
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9
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295
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DESeq2 paired design
DESeq2
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
1
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3
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167
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 5 weeks ago by 58k • written 5 weeks ago by • 0
1
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1
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96
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Different DESeq2 results
DESeq2 DifferentialExpression
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
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1
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84
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collided row names in heatmap.2
heatmap.2 genefilter deseq2
updated 5 weeks ago by 58k • written 5 weeks ago by • 0
2
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2
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174
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Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
0
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2
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109
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Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
5 weeks ago peter.zhouyu • 0
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4
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202
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Batch-corrected expression matrix NOT on a log2 scale
DESeq2 limma
updated 5 weeks ago by 3.4k • written 5 weeks ago by ▴ 60
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5
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216
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Incosistency between contrast and coef parameters in lfcShrink function
DESeq2
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
3
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1
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151
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Compare two samples by Deseqs
DESeq2 RNASeq
updated 5 weeks ago by 3.4k • written 5 weeks ago by ▴ 10
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2
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123
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DESEQ2 - compensating quality difference in replicate samples
DESeq2
6 weeks ago • updated 5 weeks ago Shail • 0
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5
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161
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Replicates in DESeq2
DESeq2
updated 21 days ago by 34k • written 5 weeks ago by • 0
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85
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Subject paired DESeq2 design
DESeq2 paired design
updated 6 weeks ago by 34k • written 6 weeks ago by ▴ 10
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2
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117
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Relative abundance of differentially abundant ASVs after DESeq2
DESeq2
6 weeks ago • updated 5 weeks ago Marion • 0
0
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4
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120
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DESeq2::DESeq(..., parallel = TRUE) fails if a partition has only genes with 0 counts across all samples
DESeq2 BiocParallel
6 weeks ago Steffi Grote • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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