Package for checking differential expression of gene

Question

[mjoyraj]

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

Answer 1

[alesssia]

Limma?

[mjoyraj]

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

[alesssia]

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.