Displaying 2 results from an estimated 2 matches for "classifytestsf".
2004 Oct 21
0
Limma B-statistics
....expBC and a
linear model fitted to the data using a design based on the three groups
(6, 5, and 5 samples in each group, respectively). I have then made 3
contrasts to cover all possible comparisons within the data set, and
generated empirical Bayes statistics using eBayes. I've then used
classifyTestsF to classify each gene according to the contrasts.
The results of all this are 23 significantly differentially expressed
genes. The moderated t-values for all these 23 genes are <0.01. However,
all the B-values are <0 (average -3!). In fact, a volcano plot of log-odds
and fold-change in th...
2007 Aug 03
4
FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
...rix(~0+targs)
> colnames(design)<-levels(targs)
> fit<-lmFit(eset.rma,design)
> cont.wt<-makeContrasts("treatment1-control","treatment2-control",level
> s=
> design)
> fit2<-contrasts.fit(fit,cont.wt)
> fit2.eb<-eBayes(fit2)
> testconts<-classifyTestsF(fit2.eb,p.value=0.01)
> topTable(fit2.eb,coef=2,n=300)
> topTable(fit2.eb,coef=1,n=300)
>
>
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