Dai, Hongying,
2012-Aug-09 15:26 UTC
[R] any recommendation for software about prediction analysis of gene expression data
Dear R users, I have a microRNA (similar to microarray) data set with gene expressions and group variables. I'd like to perform (class) prediction analysis to see which genes or gene sets predict the group variable well. I'm at the beginner level. Is there any free software in R or in point/click format that is commonly used and highly recommended? I googled this topic and found "SAM" and "PAM" packages for prediction analysis. Am I on the right track? Thanks! Dai Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital?s Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation.
R. Michael Weylandt
2012-Aug-09 16:27 UTC
[R] any recommendation for software about prediction analysis of gene expression data
I might suggest you move this question to the Bioconductor help list. (And look into bioconductor more generally) Best, Michael On Thu, Aug 9, 2012 at 10:26 AM, Dai, Hongying, <hdai at cmh.edu> wrote:> Dear R users, > > I have a microRNA (similar to microarray) data set with gene expressions and group variables. I'd like to perform (class) prediction analysis to see which genes or gene sets predict the group variable well. > > I'm at the beginner level. Is there any free software in R or in point/click format that is commonly used and highly recommended? > > I googled this topic and found "SAM" and "PAM" packages for prediction analysis. Am I on the right track? > > Thanks! > > Dai > > Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital?s Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.