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The difference when using Limma compare between 3 conditions vs 2 conditions
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Why p value inconsistent when using different number of pathway score?
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SGSeq: moving toward diffex from SGSeq analysis
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updated 4 hours ago by • 0 • written 5.5 years ago by ★ 4.0k
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Which input file is used for DGEList in EgdeR?
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updated 27 days ago by • 0 • written 15 months ago by ▴ 10
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Estimating Cell Counts for EPIC V2 array data
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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Batch correction and repeated measures
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updated 29 days ago by 50k • written 7 months ago by ▴ 10
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
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updated 14 days ago by 65k • written 2.3 years ago by • 0
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Limma design with continuous and categorical covariates
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Light difference when using coef vs omit a group when compare 3 groups.
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5 weeks ago • updated 28 days ago Chris ▴ 10
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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14 days ago • updated 10 days ago gene_bioconductor ▴ 10
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News: Bioconductor 3.19 is Released!
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15 days ago shepherl 3.9k
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FilterByExpr low counts with small sample size
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29 days ago • updated 24 days ago Jonathan ▴ 10
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Can DESeq2 rlog normalized matrix reflects time course result directly?
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Memory errors using read.bismark?
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Method to find pathways different between 2 groups
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11 days ago • updated 1 day ago Chris ▴ 10
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Create protein sequences including variants from a VCF file
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Help with running egsea()
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10 days ago • updated 8 days ago Chris ▴ 10
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News: List of Deprecated Packages for Bioc3.18
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Limma without eBayes, is it indistunguishable from Ordinary Least Square?
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Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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minfi latest update for EPIC V2 chip
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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