Is there a relatively simple and quick way to get a list of significant genes using a statistical technique like SAM? I have tried MATLAB, Limma, MaSigPro, without much luck. Any takers? Also I don't know much R.
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jimhavrilla •
2 answers
If by "quick and simple" you mean something like an online tool, you may want to look at ArrayMining or Babelomics. I have not used either of them; they just ranked highly in my Google search with some relevant keywords.
Otherwise, there are many software tools available for this task and I can only suggest you invest some effort in learning how to use them. R/Bioconductor in particular has several useful packages in the Time Course category.
Have a look at EDGE, which has a fairly simple-to-use (if a little clunky) interface, and good documentation: http://www.genomine.org/edge/ http://www.ncbi.nlm.nih.gov/pubmed/16141318
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This is for finding genes that change expression throughout senescence. Thus time course studies only or timeseries.
What do you mean by "without much luck"? What is your study design?