Detecting Up-Regulated Genes
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ANIRBAN BHAR ▴ 60
@anirban-bhar-4836
Last seen 7.2 years ago
Hi all, I have an Time-course dataset where each gene has expression values over some time-points and each time-point has some replicates. Now how can we detect up-regulated genes between two time points using some standard procedure (may be some statistical test)? I am interested to have an idea about the work-flow.. Thanks in advance.. Best Regards, Anirban [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 17 hours ago
United States
On Thu, Sep 8, 2011 at 12:06 PM, ANIRBAN BHAR <aec.ani at="" gmail.com=""> wrote: > Hi all, > > I have an Time-course dataset where each gene has expression values over > some time-points and each time-point has some replicates. Now how can we > detect up-regulated genes between two time points using some standard > procedure (may be some statistical test)? I am interested to have an idea > about the work-flow. Hi, Anirban. You might take a look at the limma package as a starting place. Your different time points will be different groups. Sean
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@freudenberg-johannes-nihniehs-e-4789
Last seen 7.2 years ago
Hi Anirban, A good start would be the limma package. > library(limma) > limmaUsersGuide() Then go to chapter 8.8 "Time Course Experiments" --Johannes -----Original Message----- From: ANIRBAN BHAR [mailto:aec.ani@gmail.com] Sent: Thursday, September 08, 2011 12:07 PM To: bioconductor at r-project.org Subject: [BioC] Detecting Up-Regulated Genes Hi all, I have an Time-course dataset where each gene has expression values over some time-points and each time-point has some replicates. Now how can we detect up-regulated genes between two time points using some standard procedure (may be some statistical test)? I am interested to have an idea about the work-flow.. Thanks in advance.. Best Regards, Anirban [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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