Showing : GAGE package • reset
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GAGE for non model organism
gage package gage
5.8 years ago melkile26 • 0
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
5.8 years ago atakanekiz ▴ 30
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Gage package; go.gset() function error: argument "go_id" is missing
gage package error
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 20
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.2 years ago by • 0 • written 6.2 years ago by • 0
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4
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1.7k
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Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 30
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DESeq2 - GAGE workflow
gage package deseq2
6.7 years ago sup230 ▴ 30
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How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
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Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
7.7 years ago joanito.liberti • 0
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Question on Gage
gage package path.ids RNA-Seq
7.7 years ago rl1385 • 0
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GAGE package statistical tests
t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment
7.8 years ago smt8n • 0
10 results • Page 1 of 1
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Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
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Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Awards • All
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Popular Question to Matthew Ritchie ▴ 1000
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