output differentially expressed genes for the interaction model to a HTML file

Share:

Description

output differentially expressed genes for the interaction model to a HTML file. It contais the following columns: ProbeID, Symbol, Description, GenBank, LocusLink, Log2ratio for each stratum, p value for each stratum, and interaction p value.

Usage

1
interaction.result2html(cdf.name, result, inter.result,filename="inter_result")

Arguments

cdf.name

cdf name which can be obtained from annotation function

result

a list of data frame returned from post.interaction function

inter.result

a data frame returned from select.sig.gene function, this is the result based on testing the interaction effect.

filename

the name of the output file

Author(s)

Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
data(testData)
normaldata<-pre.process("rma",testData)

## Create design matrix for interaction effect between "group"
## and "gender"
design.int<-make.design(pData(normaldata), c("group", "gender"), int=c(1,2))

## Create the interaction contrast
contrast.int<-make.contrast(design.int, interaction=TRUE)

## Run Regression to detect interaction effect
result.int<-regress(normaldata, design.int, contrast.int, "L")

## Select differentally expressed genes based on p.value
select.int<-select.sig.gene(result.int, p.value=0.05)

## Identify genes with the interaction effect
sig.ID<-select.int$ID[select.int$significant==TRUE]
sig.index<-match(sig.ID, rownames(exprs(normaldata)))

## Create separate tables for each level of effect modifier
result<-post.interaction("group","M", "F", design.int, normaldata[sig.index,],
  "L","none", 0.05, log2(1.5))

## Output significant result for the interaction model
interaction.result2html(annotation(normaldata), result, result.int, filename="interaction")