Question: limma p-value calculated how?
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gravatar for Kripa R
7.2 years ago by
Kripa R180
Kripa R180 wrote:
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]]
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ADD COMMENTlink modified 7.2 years ago by David Westergaard280 • written 7.2 years ago by Kripa R180
Answer: limma p-value calculated how?
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gravatar for David Westergaard
7.2 years ago by
David Westergaard280 wrote:
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
ADD COMMENTlink written 7.2 years ago by David Westergaard280
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