Showing : DESEQ • reset
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Fwd: DESeq plotting graphs.
Cancer DESeq Cancer DESeq
13.1 years ago Steve Lianoglou ★ 13k
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RNAseq object
RNASeq DESeq easyRNASeq RNASeq DESeq easyRNASeq
updated 13.1 years ago by ★ 4.2k • written 13.1 years ago by ★ 13k
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Differential expression analysis of CAGE data
Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 30
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DESeq cuont table normalization
Normalization DESeq Normalization DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 260
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DESeq - Estimating Dispersion with Technical Replicates
GLAD DESeq GLAD DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 20
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DESeq error
DESeq DESeq
updated 13.2 years ago by ★ 3.8k • written 13.2 years ago by ▴ 50
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2.8k
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DESeq - working with more than 2 conditions
DESeq DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 140
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4
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3.8k
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Estimating Size Factors in DESeq Package
DESeq DESeq
updated 13.2 years ago by ★ 3.8k • written 13.2 years ago by ▴ 20
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DESeq Fold-Change calculation
DESeq DESeq
updated 13.2 years ago by ★ 3.8k • written 13.2 years ago by ★ 1.3k
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4.5k
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RNA-seq analysis and two-way ANOVAs
edgeR baySeq DEGseq DESeq DEXSeq edgeR baySeq DEGseq DESeq DEXSeq
updated 13.2 years ago by 53k • written 13.2 years ago by ▴ 160
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how to set parameter of DESeq function estimateDispersions
DESeq DESeq
13.3 years ago wang peter ★ 2.0k
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1.5k
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deseq within and between group variation
DESeq DESeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ▴ 60
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DESeq normalization
Normalization DESeq Normalization DESeq
13.3 years ago sudeep s ▴ 60
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5
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3.0k
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EasyRNASeq issue (missing bai files)
GO PROcess DESeq easyRNASeq GO PROcess DESeq easyRNASeq
updated 13.3 years ago by ▴ 10 • written 13.3 years ago by ★ 1.2k
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how to design model in DESeq
DESeq DESeq
13.4 years ago wang peter ★ 2.0k
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796
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FW: Reproducibility in DESeq
convert DESeq convert DESeq
13.4 years ago Fatemehsadat Seyednasrollah ▴ 260
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1.3k
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DESeq installation problems
DESeq BiocInstaller DESeq BiocInstaller
updated 13.4 years ago by ★ 8.2k • written 13.4 years ago by ▴ 10
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how to get normalized counts from edgeR
DESeq DESeq
updated 13.4 years ago by ▴ 880 • written 13.4 years ago by ★ 2.0k
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easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 190
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773
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down-expression and high-expression in single cell + amplification
DESeq DESeq
13.4 years ago Dror Hibsh ▴ 40
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900
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Very Different group sizes in DE of two conditions
miRNA Cancer edgeR DESeq miRNA Cancer edgeR DESeq
updated 13.4 years ago by 53k • written 13.4 years ago by ★ 13k
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1.7k
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DESeq analysis
edgeR DESeq edgeR DESeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 260
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
13.4 years ago Gordon Smyth 53k
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FW: DESeq analysis
edgeR DESeq edgeR DESeq
13.4 years ago Fatemehsadat Seyednasrollah ▴ 260
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2.4k
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
13.4 years ago Michael Salbaum ▴ 80
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1.4k
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pvalue and padj in DESeq
DESeq DESeq
updated 13.4 years ago by ★ 3.8k • written 13.4 years ago by ★ 13k
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1.9k
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DESeq analysis
DESeq DESeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ★ 13k
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1.1k
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interactions between variables in DEXSeq
DESeq DESeq
updated 13.4 years ago by ★ 1.9k • written 13.4 years ago by ▴ 160
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estimateDispersions in DESeq
Genetics graph DESeq Genetics graph DESeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 10
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DESeq and contrasts
DESeq DESeq
updated 13.4 years ago by 53k • written 13.4 years ago by ▴ 20
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984
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RnaSeqTutorial Package
Annotation BSgenome BSgenome DESeq DEXSeq Annotation BSgenome BSgenome DESeq DEXSeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ★ 13k
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5
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1.5k
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down-expression and high-expression in single cell + amplification
DESeq DESeq
updated 13.4 years ago by ★ 4.2k • written 13.4 years ago by ★ 13k
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1.4k
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paired analysis in RNA Seq data using DESeq
RNASeq edgeR DESeq RNASeq edgeR DESeq
13.4 years ago Natasha ▴ 440
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3.8k
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voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert
updated 2.9 years ago by 53k • written 13.5 years ago by ★ 6.5k
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3
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DESeq estimateDispersions() problem
DESeq DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ★ 1.2k
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1.2k
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DESeq estimateDispersions() problem
DESeq DESeq
13.5 years ago Karl Lundén ▴ 20
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833
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DESeq error thrown during estimateDispersions w/ coxReid method
DESeq DEXSeq DESeq DEXSeq
13.5 years ago Simon Anders ★ 3.8k
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1.2k
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DESeq error with glm.fit during estimateDispersions
DESeq DESeq
updated 13.5 years ago by ★ 3.8k • written 13.5 years ago by ▴ 210
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2.0k
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How to use DESeq output to convert raw counts to normalized data
convert DESeq convert DESeq
updated 13.5 years ago by ★ 3.8k • written 13.5 years ago by ▴ 30
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9
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2.1k
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How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
Normalization DESeq Normalization DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 50
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DESeq Package Questions
Network edgeR DESeq Network edgeR DESeq
13.5 years ago Xin Davis ▴ 30
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2
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2.4k
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DESeq
DESeq DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 440
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12
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3.1k
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problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI DESeq DEXSeq GUI DESeq DEXSeq
updated 13.6 years ago by ▴ 60 • written 13.6 years ago by ▴ 370
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819
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回复： TMM factors
Normalization edgeR DESeq Normalization edgeR DESeq
13.6 years ago Mark Robinson ▴ 880
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1.3k
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DESeq without replicates, Problem trying to obtain significant hits
DESeq DESeq
13.6 years ago Asma ▴ 10
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1
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2.3k
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DeSeq - How to get the Biological Coefficient of Variation
edgeR DESeq edgeR DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 50
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2
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2.9k
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error in dispersion estimate
DESeq DESeq
13.6 years ago mariangela bonizzoni ▴ 20
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6
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1.7k
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Genominator error when calling syste.time
Genominator DESeq Genominator DESeq
updated 13.6 years ago by ★ 6.5k • written 13.6 years ago by ▴ 200
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1.5k
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question about DESeq or tissue-specific expression
DESeq DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 450
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1
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800
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Checking output of DESeq package analysis
DESeq DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ★ 13k
512 results • Page 8 of 11
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Replies
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Votes
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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