result2html {AffyExpress} | R Documentation |
output differentially expressed genes to a HTML file based on a result table from the select.sig.gene function. It contais the following columns: Probe, Symbol, Description, GenBank, LocusLink, Log2ratio, and p value.
result2html(cdf.name, result, filename="result")
cdf.name |
cdf name which can be obtained from the annotation function |
result |
a data frame returned from the gene.select function |
filename |
a file name for the output |
Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org
data(testData) normaldata<-pre.process("rma",testData) ## Create design matrix design<-make.design(pData(normaldata), "group") ## Create contrast matrix - Compare group "A" vs. "C" contrast<-make.contrast(design, "A", "C") ## Identify differentially expressed gene by using LIMMA method result<-regress(normaldata, design, contrast, "L") ## Select differentially expressed gene based on p <0.05 and ## fold change >=log2(1.5) select<-select.sig.gene(result, p.value=0.05, m.value=log2(1.5)) ## Output differentially expressed gene to a example.html result2html(annotation(normaldata), select, "example")