Showing : DEseq2 • reset
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DESEQ2 for multi-factor analysis with age(numeric), age and group
deseq2
7.2 years ago songeric1107 • 0
2
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7
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2.9k
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DESeq2 error with lfcshrink for interaction term
deseq2 interaction term
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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1
reply
657
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Unbalanced experimental design of DESeq2
DESeq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
2
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1
reply
877
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DESeq2 generating VST for Single Condition
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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1
reply
947
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Comparisons between populations
deseq2 PlotPCA draw.triple.venn
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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1
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973
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PCA analysis of 2/3 samples out of a 8 sample countmatrix
deseq2 plotpca
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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7
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2.2k
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DESeq2: Sequencing depth as confounding factor after size factor normalization
deseq2 sizefactors pca normalization library size factor
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
3
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3
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1.6k
views
DESeq2: maxCooks not set (NA)
deseq2 cooks distance dds
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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1
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1.0k
views
question about DESeq2: getVarianceStabilizedData
deseq2 software error
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
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4
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2.1k
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DESeq2 design model that considers 3 factors
deseq2 multiple factor design
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
1
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12
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2.7k
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High amount of zeros in DESeq2 RNAseq analysis
deseq2
7.2 years ago user6 • 0
2
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2
replies
2.6k
views
One-sided p-value from DESeq2
DESeq2 nbinomWaldTest one-sided p-value
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 170
0
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4
replies
1.3k
views
DESeq2 - order of covariates in the design
deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 190
1
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8
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1.6k
views
DESeq2 DEG analysis 99% overlap among LRT and specific contrasts time course no matching time point controls
deseq2 mikelove
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
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6
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3.0k
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DESeq2 replicates management
deseq2 bioconductor R
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
3
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5
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1.8k
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
2
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7
replies
3.0k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
0
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1
reply
793
views
Inconsistent results from the lfcThreshold argument?
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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12
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1.6k
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Effectiveness of normalisation if many DE genes using DESeq2
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
reply
2.4k
views
Problem with writing CollapseReplicates command
DESeq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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2
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4.3k
views
DESeqDataSetFromMatrix Unavailable for R Version 3.5.0
DESeq2 deseqdatasetfrommatrix r new version
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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1.3k
views
DESeq2 - is VSD data normalized for covariates in the model
deseq2
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 190
3
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1
reply
1.6k
views
DE genes comparison of different treatments from microarray and RNAseq data
microarray deseq2 limma edgeR
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
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6
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4.1k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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4
replies
1.5k
views
How to spot genes/transcripts in a MA-plot
ma-plot deseq2
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
1
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11
replies
2.3k
views
Need help with DESeq2's contrast feature
deseq2 michael love
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
3
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1
reply
1.0k
views
Can limma/other DE algorithms be used for differential analysis of chemical descriptors?
limma edger deseq2 cheminformatics
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
0
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1
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588
views
DGE between two related species
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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4
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681
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Problem with low reads count
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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5
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1.1k
views
DESEQ experimental design
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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3
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4.6k
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some values in assay are not integers
DESeq2 Tax4Fun
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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2
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1.6k
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lfcshrink in DESeq2 with grouping variable
deseq2 lfcshrink
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
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2
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11k
views
deseq2: convert ensembl ID to gene symbol.
DEXSeq DESeq2 DEXSeq DESeq2
updated 7.3 years ago by • 0 • written 11.3 years ago by ▴ 970
1
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5
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1.6k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
2
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10
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5.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 2.1 years ago by 43k • written 7.3 years ago by ▴ 20
2
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2
replies
1.6k
views
Looking for code showing how estimateDispersions works.
estimateDispersions deseq2
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
15
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12
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3.4k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
0
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6
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2.0k
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Using DESeq2 for T-cell receptor clonotypes
deseq2 immunology tcr clonotypes
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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1
reply
1.6k
views
Time Series Analysis
timecourse deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
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3
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1.5k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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1
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800
views
DESeq2 with HTSeq DESeqDataSetFromHTSeqCount
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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2
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585
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For multiple level variables, different results with or without subsetting
deseq2
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 10
4
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7
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9.7k
views
DESeq2: likelihood ratio test interpretation, multifactor
likelihood ratio test deseq2 LRT
updated 3.1 years ago by 43k • written 7.3 years ago by ▴ 10
0
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1
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833
views
Changes in DESeq2 Version 1.20?
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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4
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876
views
Strange results from Deseq2
deseq2
7.3 years ago swbarnes2 ★ 1.4k
0
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1
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758
views
DESeq2 relevel still gives negative log2FoldChange
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
2
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2
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15k
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Seurat/DESeq2 - single cell RNA-seq differential expression
seurat deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
2
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1
reply
842
views
DESeq2 - Three Sample Analysis
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
2
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4
replies
1.4k
views
DESeq2 on two groups
deseq2 group
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
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5
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2.1k
views
Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for slot rowRanges GenomicRangesORGRangesList
deseq2 plotCounts rowRanges
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 50
4,840 results • Page 60 of 97
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Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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