Package for checking differential expression of gene
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9.2 years ago
mjoyraj ▴ 80

I have gene expression data from five different condition. Each condition have three replicates. I want to check differential expression of gene between the conditions. Using Anova tells me overall that a gene is deferentially expressed, but it does not tell between which two or three conditions. What package will be good for such analysis

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9.2 years ago
alesssia ▴ 580

Limma?

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Can you share code for running limma. I am a novice, so having some trouble...

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The users' guide (http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf) has several examples and it's the best place to start. Please note that you should adapt these examples to your specific experimental design.

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