Showing : DESeq2 • reset
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 hours ago lonn • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 hours ago • updated 15 hours ago ussarizona • 0
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
18 hours ago quanah.hudson • 0
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42
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covariate with negative and positive values
DESeq2
1 day ago Brynn • 0
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3
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128
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 20
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3
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158
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DEG with low counts
DESeq2
3 days ago • updated 1 day ago Rajat • 0
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Deseq2 Rlog transformation
DESeq2
updated 2 days ago by ★ 4.0k • written 4 days ago by • 0
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145
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Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago hemantcnaik • 0
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100
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Bioinformatics student
Des DESeq2
updated 5 days ago by • 0 • written 5 days ago by • 0
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138
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DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago Shefali • 0
1
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1
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153
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How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by 41k • written 7 days ago by ▴ 10
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120
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 8 days ago by 41k • written 8 days ago by • 0
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2
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127
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 days ago by 65k • written 12 days ago by • 0
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2
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175
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 8 days ago by 41k • written 12 days ago by ▴ 30
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2
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210
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Regressing out batch effects
DESeq2
updated 8 days ago by 41k • written 13 days ago by • 0
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143
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DESeq2 - Missing values in count matrix
DESeq2
updated 13 days ago by 65k • written 13 days ago by • 0
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6
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388
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 14 days ago by 41k • written 14 days ago by • 0
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125
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
15 days ago • updated 14 days ago Layal • 0
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2
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139
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
15 days ago • updated 14 days ago michelafrancesconi8 • 0
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4
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209
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 15 days ago by 41k • written 16 days ago by • 0
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1
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130
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 days ago by 41k • written 20 days ago by • 0
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309
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PCA of different bacterial species
DESeq2
updated 21 days ago by 41k • written 22 days ago by ▴ 10
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2
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186
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
23 days ago Anita ▴ 10
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146
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collapseReplicates dimension error
DESeq2 Dese
updated 23 days ago by 41k • written 26 days ago by • 0
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195
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
27 days ago • updated 21 days ago Chanderkant Chaudhary • 0
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2
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194
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
28 days ago • updated 27 days ago kcarey • 0
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3
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223
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Help with Complex DESeq2 Design
DESeq2
updated 28 days ago by ★ 4.0k • written 4 weeks ago by • 0
2
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3
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267
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 28 days ago by 41k • written 4 weeks ago by ▴ 20
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1
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125
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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1
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157
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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1
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154
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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196
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
4 weeks ago feather-W • 0
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4
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396
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
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2
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223
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
0
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7
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394
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 22 days ago fr8712ca-s • 0
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2
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289
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
2
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1
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219
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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1
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196
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i'm not getting any differentially expressed genes.
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
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1
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190
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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2
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311
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DESeq2: Comparing A Knockout to a Strain
DESeq2
5 weeks ago Viktor Thiel • 0
0
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1
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193
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
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8
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362
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
5 weeks ago michelafrancesconi8 • 0
0
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1
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196
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 5 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
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4
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279
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
2
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6
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307
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Factor vs Character in design
DESeq2
6 weeks ago James Aiden • 0
1
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3
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327
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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3
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274
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Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 6 weeks ago by ▴ 10
0
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1
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226
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Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
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4
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309
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Further clarification of unbalanced group sizes DESeq2
DESeq2
6 weeks ago hmillike • 0
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2
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346
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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