Question: Multiple Sample Time Course Study Microarray Analysis
0
gravatar for jimhavrilla
6.9 years ago by
jimhavrilla10
jimhavrilla10 wrote:

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.

geo multiple microarray • 1.5k views
ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 6.9 years ago by jimhavrilla10
1

What do you mean by "without much luck"? What is your study design?

ADD REPLYlink written 6.9 years ago by Sean Davis25k

This is for finding genes that change expression throughout senescence. Thus time course studies only or timeseries.

ADD REPLYlink written 6.9 years ago by jimhavrilla10
2
gravatar for Neilfws
6.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Neilfws48k
0
gravatar for Adrian
6.9 years ago by
Adrian680
Cambridge, MA
Adrian680 wrote:

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

ADD COMMENTlink written 6.9 years ago by Adrian680
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