Limma-Contrasts-Question
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Biju Joseph ▴ 30
@biju-joseph-3955
Last seen 10.5 years ago
Dear all Sorry if this is a trivial question, My experiment design is the following 2 strains (A & B) subjected to 4 conditions each (1,2,3,4) compared using a common reference design. We are interested in various contrasts between the 8 samples. Using limma - I was able to generate topTables for the required contrasts eg: A1-B1, A2-B2, A3-B3, A4-B4 A1-A2, A2-A3, B1-B2, B2-B3 and so on A comparison for example the topTable A1-A2 and B1-B2, would represent the common response in A and B from condition 1 and condition 2. Using this manual comparison of the 2 topTables, I saw that around 400 genes are commonly differentially regulated in strain A and strain B in the conditions 1 and 2. Now when I include the following contrast in my model in limma (A1+B1)/2 - (A2+B2)/2 which in my understanding also generates the common response between condition 1 and 2 in the 2 strains A and B. The topTable generated using this contrast shows only 10 genes to be commonly differentially regulated between condition 1 and 2. Would be great if someone could explain this discrepancy to me and about which method is safer to compare(comparison of the 2 individual toptables or the toptable generated using make.contrasts). Best Biju Institut f?r Hygiene und Mikrobiologie Universit?t W?rzburg Josef-Schneider-Str. 2, Geb?ude E1 97080 W?rzburg Email: bjoseph at hygiene.uni-wuerzburg.de Tel.: 0931 201 46708 Fax: 0931 201 46445
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