Question: Package for checking differential expression of gene
0
gravatar for mjoyraj
4.2 years ago by
mjoyraj50
Taiwan
mjoyraj50 wrote:

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

R • 1.0k views
ADD COMMENTlink modified 4.2 years ago by alesssia520 • written 4.2 years ago by mjoyraj50
2
gravatar for alesssia
4.2 years ago by
alesssia520
London, UK
alesssia520 wrote:

Limma? http://bioconductor.org/packages/release/bioc/html/limma.html

ADD COMMENTlink written 4.2 years ago by alesssia520

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

ADD REPLYlink written 4.2 years ago by mjoyraj50
2

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.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by alesssia520
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