Showing : DESeq2 • reset
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DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 9 hours ago by 35k • written 1 day ago by ▴ 10
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3
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66
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 7 hours ago by 35k • written 1 day ago by • 0
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1
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47
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Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 2 days ago by 35k • written 3 days ago by • 0
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1
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51
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3 days ago by 35k • written 4 days ago by • 0
1
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2
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124
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
7 days ago • updated 6 days ago i.sudbery ▴ 20
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2
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107
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 7 days ago by ▴ 970 • written 7 days ago by • 0
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2
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126
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rlog normalised count for comparing gene expression between samples
DESeq2
7 days ago Sam • 0
1
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2
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100
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
7 days ago Bex • 0
2
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5
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164
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 8 days ago by 35k • written 10 days ago by • 0
2
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3
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116
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 8 days ago by 35k • written 9 days ago by ▴ 100
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4
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141
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DESeq treatment over baseline versus placebo over baseline methodology
DESeq2
8 days ago walter.eckalbar • 0
1
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3
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144
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 7 days ago by 35k • written 11 days ago by • 0
1
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2
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138
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DESeq2 expressed gene
DESeq2
10 days ago BioEpi • 0
0
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3
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132
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Same p-adjusted value for all samples
DESeq2 p-adjusted-value Logfoldchange
updated 12 days ago by 35k • written 12 days ago by • 0
4
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5
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196
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Help with droplevels in Deseq2
droplevels DESeq2
updated 12 days ago by ▴ 970 • written 13 days ago by • 0
1
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8
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259
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
14 days ago • updated 12 days ago dadca596 • 0
1
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3
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143
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Adding sample label to PCA plot
plotpca DESeq2
14 days ago • updated 13 days ago bjen731 • 0
3
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5
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495
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P adjusted values in Deseq2
DESeq2 Statistics
written 12 months ago by • 0
1
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1
reply
85
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TPM to raw counts
salmon DESeq2
updated 14 days ago by 13k • written 14 days ago by • 0
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1
reply
80
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Removal of sample data which belong to a different experiment
DESeq2
updated 16 days ago by 35k • written 16 days ago by • 0
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3
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170
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DESeq2: model matrix is not full rank
DESeq2
updated 17 days ago by 35k • written 17 days ago by • 0
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0
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69
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
21 days ago Jonas • 0
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2
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151
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 18 days ago by 13k • written 22 days ago by • 0
0
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1
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127
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Is it possible to specify random nested factor in DEseq2?
nested DESeq2
updated 21 days ago by 35k • written 27 days ago by • 0
2
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2
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188
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EdgeR installation issue
limma edgeR DESeq2
23 days ago • updated 22 days ago aonghus • 0
0
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2
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176
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sigh of log2FC values in DESeq2
sign FoldChange DESeq2 reference
updated 23 days ago by 35k • written 24 days ago by • 0
2
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2
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157
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Ashr and IHW
Ashr LFCShrinkage IHW DESeq2
4 weeks ago • updated 8 days ago Bex • 0
0
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7
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313
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 4 weeks ago by 35k • written 4 weeks ago by • 0
0
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2
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96
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 4 weeks ago by 35k • written 4 weeks ago by • 0
3
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2
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183
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Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
5 weeks ago mohammedtoufiq91 ▴ 10
3
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2
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175
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P-values change 100-fold with only a single count changed
DESeq2
5 weeks ago • updated 4 days ago Andrey • 0
0
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1
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116
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Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
0
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2
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149
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DESeqDataSet design issue
DESeq DESeq2
5 weeks ago matthew.valentine • 0
2
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1
reply
143
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Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
0
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1
reply
131
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
2
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3
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250
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DESeq2 - batch, condition and tissue information
DESeq2
6 weeks ago • updated 5 weeks ago Ela__77 • 0
0
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5
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263
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DESeq2 analyze MeRIP-seq
DESeq2 MeRIP-seq
updated 5 weeks ago by 35k • written 6 weeks ago by • 0
1
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2
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189
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Design formula in DESeq2
groups dispersion DESeq2 desing
6 weeks ago m.glymenaki • 0
3
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4
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224
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DESEQ2 Results log2fold and pvalue changes after removing genes
DESeq2
6 weeks ago Bine ▴ 20
0
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1
reply
109
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different results between DESeq model with multiple groups or with specific groups
DESeq2
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
0
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1
reply
126
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
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3
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176
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Error in DESeq2
DESeq2
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
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2
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251
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deseq2 datasetfrommatrix
DESeq2
updated 7 weeks ago by ▴ 970 • written 7 weeks ago by • 0
1
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1
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161
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
0
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1
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154
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Paired sample design in DESeq2
DESeq2
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
0
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9
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353
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DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
7 weeks ago michael.morash • 0
0
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5
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386
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Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 6 weeks ago by 35k • written 7 weeks ago by • 0
0
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1
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156
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values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 7 weeks ago by ▴ 970 • written 7 weeks ago by • 0
2
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2
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204
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padjust after running DESEQ2
DESeq2
7 weeks ago Bine ▴ 20
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4
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233
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Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
7 weeks ago kristoffersandas • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Need help for ProStaR Stand-alone install by benoit.marchand • 0
Thank you for answering. I've just updated to Prostar v1.26.3 and confirm that the **Prostar()** command **now works** in R for me on linu…
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Votes
Comment: Need help for ProStaR Stand-alone install
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
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