result2html: output differentially expressed genes to a HTML file

In AffyExpress: Affymetrix Quality Assessment and Analysis Tool

Description

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.

Usage

result2html(cdf.name, result, filename="result")

Arguments

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

Author(s)

Xiwei Wu [e-mail], Xuejun Arthur Li [e-mail]

Examples

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")

AffyExpress documentation built on Nov. 8, 2020, 7:50 p.m.