Hi, I'm currently using LIMMA to analyze two groups, wt vs treatment group. LIMMA says gene A is significantly different between the two groups, p=10E-6, but when I do a simple t-test I am unable to get such a significant p-value. For example my normalized values for ProbeID:A may be as followed: wt - 4.8, 5.1, 5.7 treatment - 8.1, 9.8, 7 if I do >t.test(wt, treatment) I don't get a p-value as low as what is observed in the limma top table. Why would this happen? Thanks for the help, -Kripa [[alternative HTML version deleted]]

Hello Kripa, Limma uses a moderatet t-test. If you are interested in the details, you can read more in Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3. (Copied from the limma usersguide) Best, David 2012/5/22 Kripa R <kripa777 at="" hotmail.com="">: > > Hi, I'm currently using LIMMA to analyze two groups, wt vs treatment group. LIMMA says gene A is significantly different between the two groups, p=10E-6, but when I do a simple t-test I am unable to get such a significant p-value. > > For example my normalized values for ProbeID:A may be as followed: > wt - 4.8, 5.1, 5.7 > treatment - 8.1, 9.8, 7 > > if I do >t.test(wt, treatment) I don't get a p-value as low as what is observed in the limma top table. Why would this happen? > > > > Thanks for the help, > > > -Kripa > > ? ? ? ?[[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