Showing : DeSeq2 • reset
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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429
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putting my own expression data in deseq2
DESeq2
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
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1.1k
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 months ago by ★ 4.9k • written 17 months ago by ▴ 10
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PCA plot suggestions
DESeq2 PCAtools
updated 17 months ago by 43k • written 17 months ago by • 0
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3
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1.0k
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 months ago by 43k • written 17 months ago by • 0
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 months ago by 68k • written 17 months ago by • 0
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 17 months ago by 43k • written 17 months ago by • 0
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3
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713
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Different Shrunk Log2FC according with reference
DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 20
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4
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1.0k
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
17 months ago winwater0928 • 0
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 40
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7
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
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3
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1.1k
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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439
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rlog transformation
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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1.2k
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 months ago Patadù ▴ 20
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408
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covariate with negative and positive values
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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414
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
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4
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905
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 months ago lonn • 0
0
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3
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686
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 20
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896
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How to retrieve detailed regression results from deseq2
DESeq2
18 months ago • updated 17 months ago Weiqian ▴ 10
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4
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908
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DEG with low counts
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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1
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384
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Deseq2 Rlog transformation
DESeq2
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
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2
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736
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Design Matrix within group comparison more than two groups
DESeq2
18 months ago • updated 17 months ago hemantcnaik • 0
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495
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Bioinformatics student
Des DESeq2
updated 18 months ago by • 0 • written 18 months ago by • 0
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722
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DESeq2 gives an error and R crashes
DESeq2
18 months ago Shefali • 0
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2
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773
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by ▴ 70
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1
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792
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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715
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Regressing out batch effects
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
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2
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939
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
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1
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777
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DESeq2 - Missing values in count matrix
DESeq2
updated 18 months ago by 68k • written 18 months ago by • 0
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6
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1.5k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 18 months ago by 43k • written 18 months ago by • 0
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1
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472
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
18 months ago Layal • 0
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2
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680
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
18 months ago michelafrancesconi8 • 0
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4
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1.0k
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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421
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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4
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1.3k
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PCA of different bacterial species
DESeq2
written 18 months ago by ▴ 10
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565
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collapseReplicates dimension error
DESeq2 Dese
updated 18 months ago by 43k • written 18 months ago by • 0
3
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2
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710
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
18 months ago Anita ▴ 10
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2
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821
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
18 months ago Chanderkant Chaudhary • 0
0
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2
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1.9k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
18 months ago kcarey • 0
2
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3
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769
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 20
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3
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883
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Help with Complex DESeq2 Design
DESeq2
updated 18 months ago by ★ 4.9k • written 18 months ago by • 0
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1
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673
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 18 months ago by 43k • written 18 months ago by • 0
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421
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 18 months ago by 43k • written 18 months ago by • 0
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1.5k
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
2
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2
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724
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
18 months ago feather-W • 0
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2
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1.1k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 18 months ago by 43k • written 19 months ago by • 0
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4
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837
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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7
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1.5k
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DESeq2 filtering vs edgeR filtering
DESeq2
19 months ago • updated 18 months ago fr8712ca-s • 0
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2
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3.0k
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
19 months ago • updated 18 months ago kcarey • 0
4,835 results • Page 6 of 97
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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