Entering edit mode
7.3 years ago
1769mkc
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1.2k
How can i model gene expression ? is it possible to model in way where it can be shown the expression is linear or cyclic in nature , how can i do that in R ?
You can certainly use linear models in R for gene expression (e.g., limma), but I am not sure if that's what you mean. Your post is not detailed enough I am afraid...
well i have list of genes mostly epigenetic factors and how they are expressed across various cell type from a common lineage such as haematopoietic stem cells -> monocyte as well as granulocyte and there are couple of lineage in between them.So I have the cuffdiff output data ,now i have those gene of my interest . So certain genes might be expressed once and at the same time some other genes might be expressed in all lineage type may be cyclic fashion .
So thats my basic idea ,can you now let me know how can i put forth my idea in R since I believe I have to prepare my data sets accordingly .if you can give me some idea or basic R code layout i can have a primer to start and proceed
If you want my advice: get the raw read counts direct from your BAM files, skip cuffdiff analysis, and use limma or edgeR.
Read the user's guide for limma or edgeR first, they are very educative.
Hi krushnach80,
Try to be as informative as possible in your posts, so put this information there from the beginning and don't make us ask for it.
Cheers,
Wouter