limmaCompleteTest {DAPAR} | R Documentation |
This function is a limmaCompleteTest
limmaCompleteTest(qData, Conditions, RepBio, RepTech, Contrast = 1)
qData |
A matrix of quantitative data, without any missing values. |
Conditions |
A vector of factor which indicates the name of the biological condition for each replicate. |
RepBio |
A vector of factor which indicates the number of the bio rep for each replicate. |
RepTech |
A vector of factor which indicates the number of the tech rep for each replicate. |
Contrast |
Indicates if the test consists of the comparison of each biological condition versus each of the other ones (Contrast=1; for example H0:"C1=C2" vs H1:"C1!=C2", etc.) or each condition versus all others (Contrast=2; e.g. H0:"C1=(C2+C3)/2" vs H1:"C1!=(C2+C3)/2", etc. if there are three conditions). |
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Quentin Giai-Gianetto
require(DAPARdata) data(Exp1_R25_pept) obj <- wrapper.mvImputation(Exp1_R25_pept[1:1000], "QRILC") condition1 <- '25fmol' condition2 <- '10fmol' qData <- Biobase::exprs(obj) RepBio <- RepTech <- factor(1:6) conds <- factor(c(rep(condition1, 3), (rep(condition2, 3)))) limma <- limmaCompleteTest(qData,conds,RepBio, RepTech)