[R] Statistical Questions: finding differentially expressed genes

From: Keizer_71 <christophe.lo_at_gmail.com>
Date: Thu, 06 Mar 2008 06:46:07 -0800 (PST)

Hi Everyone,

I am trying to find a way to do this in excel to tell me which genes are the most differentially expressed. Sorry, i couldn't find excel forum section in nabble. However, if it is in R it is fine. This is a microarray data, and it has been normalized. According to Dov Stekel in Microarray, i will need to calculate log ratio (control-treatment). Once you have the log ratio, calculate using paired t-test. Once you calculate the paired t-test, you will find the p-value and the t-test. Is there a way in excel to calculate the confidence level that is significant. For example, it will be under 1% for all the genes to be differentially expressed.

The book did not explained how log ratio will help me determine the significant value.

GeneID treatment control treatment control treatment control

Gene1        2.1   1 2     2.2     1.1    0.7      2.7 
Gene2        1.5   1.4   1.7    2.2   1.3     1.2 
Gene3      1.4   1.7   1.8    2.7   1.6      1.5 
Gene4       2.2   2.4    2.1    2.3     2.1      1.9 
Gene5       2.6   3.4    2.1    1.3   2.6     2.9 

Objective: find genes who are differentially epxressed.

View this message in context: http://www.nabble.com/Statistical-Questions%3A-finding-differentially-expressed-genes-tp15873163p15873163.html
Sent from the R help mailing list archive at Nabble.com.

R-help_at_r-project.org mailing list
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Received on Thu 06 Mar 2008 - 15:44:40 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 10 Mar 2008 - 11:30:21 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive