Bioconductor GAGE package

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gage package gage

5.8 years ago melkile26 • 0

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gage gage package gene expression matrix gene set analysis

5.8 years ago atakanekiz ▴ 30

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2.8k

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gage package error

updated 6.0 years ago by James W. MacDonald 65k • written 6.0 years ago by Miskey, Csaba ▴ 20

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gage gage package pathview rna-seq

updated 2.2 years ago by Helen • 0 • written 6.2 years ago by tarun2 • 0

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1.7k

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kegg geneset genelist gage package

updated 6.7 years ago by Gordon Smyth 50k • written 6.7 years ago by sup230 ▴ 30

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1.5k

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gage package deseq2

6.8 years ago sup230 ▴ 30

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1.6k

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gage gage package

updated 7.5 years ago by Luo Weijun ★ 1.6k • written 7.6 years ago by Michael • 0

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1.4k

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R gage package rnaseq pathview

7.7 years ago joanito.liberti • 0

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936

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gage package path.ids RNA-Seq

7.8 years ago rl1385 • 0

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914

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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: Cannot connect to ExperimentHub server by Jiayu • 0

Many thanks and it also resolved the same issue for me!

Comment: Help with running egsea() by Chris • 0

I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…

Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0

Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…

Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k

sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…

Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k

I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?

Votes

Answer: minfi latest update for EPIC V2 chip

A: Error in DESeqDataSet : some values in assay are not integers

Answer: Cannot connect to ExperimentHub server

Answer: confused with tximport counts abundance using salmon input

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call

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Popular Question to Gyan Prakash Mishra ▴ 10