Showing : DEseq • reset
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 13 hours ago by ★ 2.0k • written 1 day ago by • 0
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104
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 9 days ago by ★ 1.5k • written 11 days ago by • 0
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 11.0 years ago by ▴ 190
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173
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 4 months ago by ★ 2.0k • written 4 months ago by • 0
3
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2
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285
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
6 months ago manwar • 0
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278
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 7 months ago by 39k • written 7 months ago by • 0
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5
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404
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Error in DEseq
DEseq RNASeqData
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
2
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1
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442
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 8 months ago by ★ 1.2k • written 8 months ago by • 0
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5
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583
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Potential outlier/high variance
deseq DESeq2
updated 9 months ago by 39k • written 9 months ago by • 0
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2
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330
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Deseq2 with imbalanced design
Deseq
10 months ago Alex • 0
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 11 months ago by • 0 • written 2.8 years ago by ▴ 10
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2.3k
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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 27 days ago by 47k • written 10.7 years ago by 6.5k
12 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot by Nathalie • 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Comment: Design for DE analysis in tidybulk by Michael Love 39k
The mapping from what you want to a contrast is a long conversation. You can make pairwise comparisons or numeric contrasts or really anyth…
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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