Note for the above table:
The ANOVA calculations are based on Mixed Model of Wolfinger, et al.
The FDR is based on Benjamini and Hochberg.
The columns and their meaning:
GeneName: gene identifier, coming from the Agilent arrays.
Treat: sample name.
_Treat: sample name: these two columns indicate which two samples the present row/record is comaring
Estimate: log (base e=2.7183) ratio of Treat and _Treat. i.e. log (Treat/_Treat). Positive number means the gene is “up” in “Treat” and down in “_Treat”.
StdErr: error bar of the Estimate (log ratio).
DF: number of degrees of freedom; it the total number of data points minus the number of parameters in the ANOVA model.
tValue: Estimate/StdErr.
Probt: p-value, the probability that the pair of samples (Treat and _Treat) is not differentially expressed. Smaller p-value indicates that the pair of samples is differentially expressed.
FalseDiscoveryRate(FDR) : calculated using Benjamini & Hochberg method. It describes the percentage of false positives at the threshold of p-value. |
